Source Name	Provider	Material Type	Term Source REF	Characteristics[Organism]	Term Source REF	Characteristics[Sex]	Term Source REF	Characteristics[DiseaseState]	Term Source REF	Sample Name	Material Type	Term Source REF	Characteristics[OrganismPart]	Term Source REF	Description	Protocol REF	Performer	Extract Name	Material Type	Term Source REF	Comment[SRA_SAMPLE]	Protocol REF	Performer	Extract Name	Comment[LIBRARY_LAYOUT]	Comment[LIBRARY_SOURCE]	Comment[LIBRARY_STRATEGY]	Comment[LIBRARY_SELECTION]	Comment[NOMINAL_LENGTH]	Comment[LIBRARY_NAME]	Comment[SRA_EXPERIMENT]	Description	Protocol REF	Performer	Date	Assay Name	Technology Type	Term Source REF	Comment[SPOT_LENGTH]	Protocol REF	Parameter Value[Software Versions]	Scan Name	Comment[SRA_RUN]	Comment[SRA_FILE_URI]	Comment[OCG Data Level]	Protocol REF	Derived Array Data File	Comment[SRA_RUN]	Comment[SRA_FILE_URI]	Comment[OCG Data Level]	Comment[ASSEMBLY_NAME]	Protocol REF	Derived Array Data File	Comment[OCG Data Level]
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-14	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..10.fastq	SRR315943	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315943/SRR315943.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-14	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..11.fastq	SRR315944	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315944/SRR315944.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-15	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..12.fastq	SRR315945	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315945/SRR315945.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-15	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..13.fastq	SRR315946	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315946/SRR315946.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-15	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..14.fastq	SRR315947	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315947/SRR315947.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-15	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..15.fastq	SRR315948	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315948/SRR315948.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01413 A01413 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01413-1..4.fastq	SRR315949	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315949/SRR315949.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01413 A01413 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01413-1..5.fastq	SRR315950	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315950/SRR315950.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01413 A01413 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01413-1..6.fastq	SRR315951	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315951/SRR315951.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-14	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..8.fastq	SRR315952	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315952/SRR315952.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-14	A01413 A01413 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01413-1..9.fastq	SRR315953	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR315953/SRR315953.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01413	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413	DNA	EFO	SRS405358	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01413 A01413 library	PAIRED	GENOMIC	WGS	RANDOM		A01413	SRX084960	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01413 A01413 run	sequencing assay	EFO	194	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01413-bam.bam	SRR390368	@dbgap@:reads/SRP020237/SRS405358/SRX084960/SRR390368/SRR390368.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01413_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-32947	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01414	organism part	EFO	Solid Tumor	NCIt	"INTESTINE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01414	DNA	EFO	SRS405535	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01414 A01414 library	SINGLE	GENOMIC	WGS	RANDOM		A01414	SRX101052	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01414 A01414 run	sequencing assay	EFO	178	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01414-1..10.bam	SRR352730	@dbgap@:reads/SRP020237/SRS405535/SRX101052/SRR352730/SRR352730.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01414_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..fastq	SRR315954	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315954/SRR315954.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..1.fastq	SRR315955	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315955/SRR315955.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..10.fastq	SRR315956	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315956/SRR315956.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..11.fastq	SRR315957	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315957/SRR315957.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..12.fastq	SRR315958	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315958/SRR315958.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..13.fastq	SRR315959	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315959/SRR315959.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..14.fastq	SRR315960	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315960/SRR315960.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..15.fastq	SRR315961	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315961/SRR315961.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..2.fastq	SRR315962	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315962/SRR315962.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..3.fastq	SRR315963	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315963/SRR315963.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..4.fastq	SRR315964	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315964/SRR315964.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..5.fastq	SRR315965	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315965/SRR315965.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..6.fastq	SRR315966	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315966/SRR315966.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..7.fastq	SRR315967	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315967/SRR315967.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..8.fastq	SRR315968	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315968/SRR315968.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-02	A01415 A01415 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01415-1..9.fastq	SRR315969	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR315969/SRR315969.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01415	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415	DNA	EFO	SRS405359	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01415 A01415 library	PAIRED	GENOMIC	WGS	RANDOM		A01415	SRX084961	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01415 A01415 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01415-bam.bam	SRR390360	@dbgap@:reads/SRP020237/SRS405359/SRX084961/SRR390360/SRR390360.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01415_16_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..fastq	SRR315970	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315970/SRR315970.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..1.fastq	SRR315971	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315971/SRR315971.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-04-06	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.1	A01416-1..10.fastq	SRR315972	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315972/SRR315972.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..2.fastq	SRR315973	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315973/SRR315973.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..3.fastq	SRR315974	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315974/SRR315974.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..4.fastq	SRR315975	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315975/SRR315975.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..5.fastq	SRR315976	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315976/SRR315976.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..6.fastq	SRR315977	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315977/SRR315977.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01416 A01416 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01416-1..7.fastq	SRR315978	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315978/SRR315978.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-03-25	A01416 A01416 run	sequencing assay	EFO	50	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.1	A01416-1..8.fastq	SRR315979	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR315979/SRR315979.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01416	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416	DNA	EFO	SRS405360	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01416 A01416 library	PAIRED	GENOMIC	WGS	RANDOM		A01416	SRX084962	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01416 A01416 run	sequencing assay	EFO	175	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01416-bam.bam	SRR390363	@dbgap@:reads/SRP020237/SRS405360/SRX084962/SRR390363/SRR390363.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01416_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-24395	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01417	organism part	EFO	Solid Tumor	NCIt	"SPLEEN"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01417	DNA	EFO	SRS405534	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01417 A01417 library	PAIRED	GENOMIC	WGS	RANDOM		A01417	SRX101053	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-06	A01417 A01417 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01417-1..bam	SRR352740	@dbgap@:reads/SRP020237/SRS405534/SRX101053/SRR352740/SRR352740.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01417_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..fastq	SRR315980	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315980/SRR315980.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..1.fastq	SRR315981	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315981/SRR315981.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..2.fastq	SRR315982	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315982/SRR315982.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..3.fastq	SRR315983	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315983/SRR315983.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..4.fastq	SRR315984	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315984/SRR315984.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..5.fastq	SRR315985	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315985/SRR315985.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..6.fastq	SRR315986	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315986/SRR315986.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01418 A01418 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01418-1..7.fastq	SRR315987	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR315987/SRR315987.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418	DNA	EFO	SRS405361	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01418 A01418 library	PAIRED	GENOMIC	WGS	RANDOM		A01418	SRX084963	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01418 A01418 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01418-bam.bam	SRR390369	@dbgap@:reads/SRP020237/SRS405361/SRX084963/SRR390369/SRR390369.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01418_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-24915	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01419	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01419	DNA	EFO	SRS405536	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01419 A01419 library	PAIRED	GENOMIC	WGS	RANDOM		A01419	SRX101054	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-04	A01419 A01419 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01419-1-bam.bam	SRR352749	@dbgap@:reads/SRP020237/SRS405536/SRX101054/SRR352749/SRR352749.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01419_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-30145	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01420	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01420	DNA	EFO	SRS266284	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01420 A01420 library	PAIRED	GENOMIC	WGS	RANDOM		A01420	SRX198289	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01420 A01420 run	sequencing assay	EFO	199	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01420_9_lanes_dupsFlagged.bam	SRR598755	@dbgap@:reads/SRP020237/SRS266284/SRX198289/SRR598755/SRR598755.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01420_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-10398	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01421	organism part	EFO	Solid Tumor	NCIt	"ENT SOFT TISSUE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01421	DNA	EFO	SRS405537	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01421 A01421 library	PAIRED	GENOMIC	WGS	RANDOM		A01421	SRX101055	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-11	A01421 A01421 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01421-1..bam	SRR352757	@dbgap@:reads/SRP020237/SRS405537/SRX101055/SRR352757/SRR352757.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01421_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-24904	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01422	organism part	EFO	Solid Tumor	NCIt	"THYROID"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01422	DNA	EFO	SRS266286	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01422 A01422 library	PAIRED	GENOMIC	WGS	RANDOM		A01422	SRX198297	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01422 A01422 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01422_11_lanes_dupsFlagged.bam	SRR598763	@dbgap@:reads/SRP020237/SRS266286/SRX198297/SRR598763/SRR598763.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01422_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
81-52884	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01423	organism part	EFO	Solid Tumor	NCIt	"BREAST"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01423	DNA	EFO	SRS405538	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01423 A01423 library	PAIRED	GENOMIC	WGS	RANDOM		A01423	SRX101056	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-14	A01423 A01423 run	sequencing assay	EFO	182	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01423-1..bam	SRR352768	@dbgap@:reads/SRP020237/SRS405538/SRX101056/SRR352768/SRR352768.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01423_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..fastq	SRR315988	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315988/SRR315988.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..1.fastq	SRR315989	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315989/SRR315989.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..2.fastq	SRR315990	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315990/SRR315990.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..3.fastq	SRR315991	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315991/SRR315991.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..4.fastq	SRR315992	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315992/SRR315992.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..5.fastq	SRR315993	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315993/SRR315993.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..6.fastq	SRR315994	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315994/SRR315994.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01424 A01424 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01424-1..7.fastq	SRR315995	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR315995/SRR315995.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01424	organism part	EFO	Solid Tumor	NCIt	"TONSIL"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424	DNA	EFO	SRS405363	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01424 A01424 library	PAIRED	GENOMIC	WGS	RANDOM		A01424	SRX084964	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01424 A01424 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01424-bam.bam	SRR390370	@dbgap@:reads/SRP020237/SRS405363/SRX084964/SRR390370/SRR390370.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01424_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
02-20170	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01425	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01425	DNA	EFO	SRS266288	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01425 A01425 library	PAIRED	GENOMIC	WGS	RANDOM		A01425	SRX198296	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01425 A01425 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01425_13_lanes_dupsFlagged.bam	SRR598761	@dbgap@:reads/SRP020237/SRS266288/SRX198296/SRR598761/SRR598761.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01425_13_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01426 A01426 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..fastq	SRR315996	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR315996/SRR315996.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01426 A01426 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..1.fastq	SRR315997	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR315997/SRR315997.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01426 A01426 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..10.fastq	SRR315998	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR315998/SRR315998.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01426 A01426 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..11.fastq	SRR315999	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR315999/SRR315999.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-23	A01426 A01426 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..12.fastq	SRR316000	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR316000/SRR316000.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01426 A01426 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..2.fastq	SRR316001	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR316001/SRR316001.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01426 A01426 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..3.fastq	SRR316002	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR316002/SRR316002.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01426 A01426 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..8.fastq	SRR316003	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR316003/SRR316003.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01426 A01426 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01426-1..9.fastq	SRR316004	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR316004/SRR316004.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-09-13	A01426 A01426 run	sequencing assay	EFO	205	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2	A01426-1..14.fastq	SRR380840	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR380840/SRR380840.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01426	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426	DNA	EFO	SRS405362	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01426 A01426 library	PAIRED	GENOMIC	WGS	RANDOM		A01426	SRX084965	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01426 A01426 run	sequencing assay	EFO	184	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01426_10_lanes_dupsFlagged.bam	SRR766829	@dbgap@:reads/SRP020237/SRS405362/SRX084965/SRR766829/SRR766829.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01426_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
99-27137	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01427	organism part	EFO	Solid Tumor	NCIt	"STOMACH"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01427	DNA	EFO	SRS266289	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01427 A01427 library	PAIRED	GENOMIC	WGS	RANDOM		A01427	SRX198292	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01427 A01427 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01427_10_lanes_dupsFlagged.bam	SRR598758	@dbgap@:reads/SRP020237/SRS266289/SRX198292/SRR598758/SRR598758.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01427_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
09-41082	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01428	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01428	DNA	EFO	SRS405539	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01428 A01428 library	SINGLE	GENOMIC	WGS	RANDOM		A01428	SRX101057	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-28	A01428 A01428 run	sequencing assay	EFO	163	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01428-1..1.bam	SRR352782	@dbgap@:reads/SRP020237/SRS405539/SRX101057/SRR352782/SRR352782.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01428_A04044_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
07-25012	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01429	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01429	DNA	EFO	SRS405540	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01429 A01429 library	PAIRED	GENOMIC	WGS	RANDOM	382	A01429	SRX101058	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01429 A01429 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01429_8_lanes_dupsFlagged.bam	SRR390851	@dbgap@:reads/SRP020237/SRS405540/SRX101058/SRR390851/SRR390851.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01429_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-33777	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01430	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01430	DNA	EFO	SRS405541	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01430 A01430 library	PAIRED	GENOMIC	WGS	RANDOM	377	A01430	SRX101059	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01430 A01430 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01430_10_lanes_dupsFlagged.bam	SRR556082	@dbgap@:reads/SRP020237/SRS405541/SRX101059/SRR556082/SRR556082.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01430_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
08-25894	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01431	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01431	DNA	EFO	SRS405542	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01431 A01431 library	PAIRED	GENOMIC	WGS	RANDOM		A01431	SRX101060	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01431 A01431 run	sequencing assay	EFO	149	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01431_9_lanes_dupsFlagged.bam	SRR390853	@dbgap@:reads/SRP020237/SRS405542/SRX101060/SRR390853/SRR390853.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01431_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
07-25012	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01432	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01432	DNA	EFO	SRS405543	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01432 A01432 library	PAIRED	GENOMIC	WGS	RANDOM		A01432	SRX101061	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01432 A01432 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01432_8_lanes_dupsFlagged.bam	SRR390854	@dbgap@:reads/SRP020237/SRS405543/SRX101061/SRR390854/SRR390854.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01432_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-33777	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01433	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01433	DNA	EFO	SRS405544	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01433 A01433 library	PAIRED	GENOMIC	WGS	RANDOM	375	A01433	SRX101062	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01433 A01433 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01433_8_lanes_dupsFlagged.bam	SRR390850	@dbgap@:reads/SRP020237/SRS405544/SRX101062/SRR390850/SRR390850.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01433_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01434-1..fastq	SRR316005	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316005/SRR316005.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01434-1..1.fastq	SRR316006	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316006/SRR316006.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01434-1..2.fastq	SRR316007	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316007/SRR316007.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01434-1..3.fastq	SRR316008	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316008/SRR316008.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01434 A01434 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01434-1..4.fastq	SRR316009	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316009/SRR316009.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01434 A01434 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01434-1..5.fastq	SRR316010	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316010/SRR316010.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01434 A01434 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01434-1..6.fastq	SRR316011	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316011/SRR316011.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01434 A01434 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01434-1..7.fastq	SRR316012	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR316012/SRR316012.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-22	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06665-1..fastq	SRR353120	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR353120/SRR353120.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-11	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06665-1..1.fastq	SRR353121	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR353121/SRR353121.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-11	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06665-1..2.fastq	SRR353122	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR353122/SRR353122.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-11	A01434 A01434 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06665-1..3.fastq	SRR353123	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR353123/SRR353123.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01434	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434	DNA	EFO	SRS405364	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01434 A01434 library	PAIRED	GENOMIC	WGS	RANDOM		A01434	SRX084966	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01434 A01434 run	sequencing assay	EFO	191	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01434-bam.bam	SRR390372	@dbgap@:reads/SRP020237/SRS405364/SRX084966/SRR390372/SRR390372.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01434_A06665_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01435	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01435	DNA	EFO	SRS405545	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01435 A01435 library	PAIRED	GENOMIC	WGS	RANDOM		A01435	SRX101063	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-23	A01435 A01435 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01435-1..10.bam	SRR352826	@dbgap@:reads/SRP020237/SRS405545/SRX101063/SRR352826/SRR352826.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01435_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01436-1..fastq	SRR316013	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316013/SRR316013.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01436-1..1.fastq	SRR316014	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316014/SRR316014.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01436-1..2.fastq	SRR316015	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316015/SRR316015.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-29	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01436-1..3.fastq	SRR316016	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316016/SRR316016.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01436 A01436 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01436-1..4.fastq	SRR316017	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316017/SRR316017.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01436 A01436 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01436-1..5.fastq	SRR316018	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316018/SRR316018.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01436 A01436 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01436-1..6.fastq	SRR316019	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316019/SRR316019.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-01	A01436 A01436 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.8.0	A01436-1..7.fastq	SRR316020	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR316020/SRR316020.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06666-1..2.fastq	SRR353124	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR353124/SRR353124.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-08-05	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2	A06666-1..3.fastq	SRR353125	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR353125/SRR353125.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-08-05	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2	A06666-1..4.fastq	SRR353126	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR353126/SRR353126.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-08-05	A01436 A01436 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2	A06666-1..5.fastq	SRR353127	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR353127/SRR353127.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-15256	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01436	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436	DNA	EFO	SRS405365	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01436 A01436 library	PAIRED	GENOMIC	WGS	RANDOM		A01436	SRX084967	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01436 A01436 run	sequencing assay	EFO	192	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01436-bam.bam	SRR390373	@dbgap@:reads/SRP020237/SRS405365/SRX084967/SRR390373/SRR390373.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01436_A06666_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..fastq	SRR316021	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316021/SRR316021.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..1.fastq	SRR316022	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316022/SRR316022.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..2.fastq	SRR316023	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316023/SRR316023.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-18	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..5.fastq	SRR316024	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316024/SRR316024.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-18	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..6.fastq	SRR316025	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316025/SRR316025.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-21	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..7.fastq	SRR316026	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316026/SRR316026.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-21	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..8.fastq	SRR316027	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316027/SRR316027.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-21	A01437 A01437 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01437-1..9.fastq	SRR316028	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR316028/SRR316028.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25439	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01437	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437	DNA	EFO	SRS405366	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01437 A01437 library	PAIRED	GENOMIC	WGS	RANDOM	429	A01437	SRX084968	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01437 A01437 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01437-bam.bam	SRR390375	@dbgap@:reads/SRP020237/SRS405366/SRX084968/SRR390375/SRR390375.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01437_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-30025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01438	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01438	DNA	EFO	SRS405546	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01438 A01438 library	PAIRED	GENOMIC	WGS	RANDOM	409	A01438	SRX101064	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-21	A01438 A01438 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01438-1..bam	SRR352835	@dbgap@:reads/SRP020237/SRS405546/SRX101064/SRR352835/SRR352835.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01438_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..10.fastq	SRR316029	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316029/SRR316029.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..11.fastq	SRR316030	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316030/SRR316030.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..12.fastq	SRR316031	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316031/SRR316031.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..13.fastq	SRR316032	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316032/SRR316032.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..14.fastq	SRR316033	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316033/SRR316033.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..15.fastq	SRR316034	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316034/SRR316034.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..16.fastq	SRR316035	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316035/SRR316035.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..8.fastq	SRR316036	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316036/SRR316036.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-27	A01439 A01439 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01439-1..9.fastq	SRR316037	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR316037/SRR316037.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-11535	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01439	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439	DNA	EFO	SRS405367	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01439 A01439 library	PAIRED	GENOMIC	WGS	RANDOM	374	A01439	SRX084969	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01439 A01439 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01439-bam.bam	SRR390364	@dbgap@:reads/SRP020237/SRS405367/SRX084969/SRR390364/SRR390364.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01439_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-24915	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01440	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01440	DNA	EFO	SRS405547	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01440 A01440 library	PAIRED	GENOMIC	WGS	RANDOM	420	A01440	SRX101065	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-04	A01440 A01440 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01440-1..bam	SRR352844	@dbgap@:reads/SRP020237/SRS405547/SRX101065/SRR352844/SRR352844.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01440_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-30145	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01441	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01441	DNA	EFO	SRS405548	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01441 A01441 library	PAIRED	GENOMIC	WGS	RANDOM	445	A01441	SRX101066	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-04	A01441 A01441 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01441-1..bam	SRR352852	@dbgap@:reads/SRP020237/SRS405548/SRX101066/SRR352852/SRR352852.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01441_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-10398	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01442	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01442	DNA	EFO	SRS405549	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01442 A01442 library	PAIRED	GENOMIC	WGS	RANDOM	397	A01442	SRX101067	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-11	A01442 A01442 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01442-1..bam	SRR352860	@dbgap@:reads/SRP020237/SRS405549/SRX101067/SRR352860/SRR352860.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01442_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-32947	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01443	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01443	DNA	EFO	SRS266301	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01443 A01443 library	PAIRED	GENOMIC	WGS	RANDOM		A01443	SRX198287	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01443 A01443 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01443_9_lanes_dupsFlagged.bam	SRR598752	@dbgap@:reads/SRP020237/SRS266301/SRX198287/SRR598752/SRR598752.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01443_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-24395	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01444	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01444	DNA	EFO	SRS405550	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01444 A01444 library	PAIRED	GENOMIC	WGS	RANDOM	410	A01444	SRX101068	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-06	A01444 A01444 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01444-1..bam	SRR352869	@dbgap@:reads/SRP020237/SRS405550/SRX101068/SRR352869/SRR352869.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01444_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..fastq	SRR316038	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316038/SRR316038.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..1.fastq	SRR316039	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316039/SRR316039.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..2.fastq	SRR316040	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316040/SRR316040.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..3.fastq	SRR316041	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316041/SRR316041.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..4.fastq	SRR316042	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316042/SRR316042.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..5.fastq	SRR316043	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316043/SRR316043.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..6.fastq	SRR316044	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316044/SRR316044.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-17	A01445 A01445 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01445-1..7.fastq	SRR316045	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR316045/SRR316045.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01445	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445	DNA	EFO	SRS405368	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01445 A01445 library	PAIRED	GENOMIC	WGS	RANDOM		A01445	SRX084970	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01445 A01445 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01445-bam.bam	SRR390374	@dbgap@:reads/SRP020237/SRS405368/SRX084970/SRR390374/SRR390374.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01445_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
81-52884	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01446	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01446	DNA	EFO	SRS405551	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01446 A01446 library	PAIRED	GENOMIC	WGS	RANDOM		A01446	SRX101069	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-14	A01446 A01446 run	sequencing assay	EFO	177	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01446-1..bam	SRR352878	@dbgap@:reads/SRP020237/SRS405551/SRX101069/SRR352878/SRR352878.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01446_11_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..fastq	SRR316046	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316046/SRR316046.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..1.fastq	SRR316047	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316047/SRR316047.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..2.fastq	SRR316048	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316048/SRR316048.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..3.fastq	SRR316049	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316049/SRR316049.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..4.fastq	SRR316050	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316050/SRR316050.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..5.fastq	SRR316051	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316051/SRR316051.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..6.fastq	SRR316052	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316052/SRR316052.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-16	A01447 A01447 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01447-1..7.fastq	SRR316053	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR316053/SRR316053.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-19919	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01447	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447	DNA	EFO	SRS405369	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01447 A01447 library	PAIRED	GENOMIC	WGS	RANDOM		A01447	SRX084971	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01447 A01447 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01447-bam.bam	SRR390376	@dbgap@:reads/SRP020237/SRS405369/SRX084971/SRR390376/SRR390376.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01447_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
08-25894	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01448	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01448	DNA	EFO	SRS405552	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01448 A01448 library	PAIRED	GENOMIC	WGS	RANDOM	390	A01448	SRX101070	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-04-06	A01448 A01448 run	sequencing assay	EFO	157	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.1					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01448-1..14.bam	SRR352889	@dbgap@:reads/SRP020237/SRS405552/SRX101070/SRR352889/SRR352889.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01448_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
99-27137	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01449	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01449	DNA	EFO	SRS405553	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01449 A01449 library	PAIRED	GENOMIC	WGS	RANDOM		A01449	SRX101071	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-15	A01449 A01449 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01449-1..10.bam	SRR352896	@dbgap@:reads/SRP020237/SRS405553/SRX101071/SRR352896/SRR352896.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01449_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
02-20170	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01450	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01450	DNA	EFO	SRS405554	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01450 A01450 library	PAIRED	GENOMIC	WGS	RANDOM	420	A01450	SRX101072	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-25	A01450 A01450 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01450-1..bam	SRR352905	@dbgap@:reads/SRP020237/SRS405554/SRX101072/SRR352905/SRR352905.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01450_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-25674	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01451	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01451	DNA	EFO	SRS405555	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01451 A01451 library	PAIRED	GENOMIC	WGS	RANDOM	409	A01451	SRX101073	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-07	A01451 A01451 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01451-1..bam	SRR352913	@dbgap@:reads/SRP020237/SRS405555/SRX101073/SRR352913/SRR352913.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01451_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..fastq	SRR316054	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316054/SRR316054.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..1.fastq	SRR316055	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316055/SRR316055.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..2.fastq	SRR316056	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316056/SRR316056.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..3.fastq	SRR316057	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316057/SRR316057.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..4.fastq	SRR316058	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316058/SRR316058.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..5.fastq	SRR316059	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316059/SRR316059.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..6.fastq	SRR316060	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316060/SRR316060.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-16	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..7.fastq	SRR316061	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316061/SRR316061.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-23	A01452 A01452 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01452-1..8.fastq	SRR316062	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR316062/SRR316062.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-22057	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01452	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452	DNA	EFO	SRS405370	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01452 A01452 library	PAIRED	GENOMIC	WGS	RANDOM	401	A01452	SRX084972	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01452 A01452 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01452-bam.bam	SRR390361	@dbgap@:reads/SRP020237/SRS405370/SRX084972/SRR390361/SRR390361.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01452_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01453 A01453 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..fastq	SRR316063	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316063/SRR316063.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01453 A01453 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..1.fastq	SRR316064	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316064/SRR316064.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01453 A01453 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..10.fastq	SRR316065	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316065/SRR316065.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01453 A01453 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..11.fastq	SRR316066	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316066/SRR316066.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01453 A01453 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..2.fastq	SRR316067	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316067/SRR316067.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-12-17	A01453 A01453 run	sequencing assay	EFO	161	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..3.fastq	SRR316068	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316068/SRR316068.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01453 A01453 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..8.fastq	SRR316069	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316069/SRR316069.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01453 A01453 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A01453-1..9.fastq	SRR316070	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR316070/SRR316070.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-12939	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01453	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453	DNA	EFO	SRS405371	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01453 A01453 library	PAIRED	GENOMIC	WGS	RANDOM	392	A01453	SRX084973	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A01453 A01453 run	sequencing assay	EFO	182	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01453-bam.bam	SRR390377	@dbgap@:reads/SRP020237/SRS405371/SRX084973/SRR390377/SRR390377.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01453_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
09-41082	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01454	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01454	DNA	EFO	SRS405556	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01454 A01454 library	SINGLE	GENOMIC	WGS	RANDOM		A01454	SRX101074	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-28	A01454 A01454 run	sequencing assay	EFO	137	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01454-1..1.bam	SRR352921	@dbgap@:reads/SRP020237/SRS405556/SRX101074/SRR352921/SRR352921.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01454_A04045_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
05-24904	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01455	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01455	DNA	EFO	SRS405558	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01455 A01455 library	PAIRED	GENOMIC	WGS	RANDOM	459	A01455	SRX101075	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-13	A01455 A01455 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01455-1..bam	SRR352928	@dbgap@:reads/SRP020237/SRS405558/SRX101075/SRR352928/SRR352928.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01455_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
04-29264	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01456	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01456	DNA	EFO	SRS266310	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01456 A01456 library	PAIRED	GENOMIC	WGS	RANDOM		A01456	SRX198290	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01456 A01456 run	sequencing assay	EFO	199	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01456_10_lanes_dupsFlagged.bam	SRR598756	@dbgap@:reads/SRP020237/SRS266310/SRX198290/SRR598756/SRR598756.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01456_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-34043	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01457	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01457	DNA	EFO	SRS405557	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01457 A01457 library	PAIRED	GENOMIC	WGS	RANDOM		A01457	SRX101076	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-21	A01457 A01457 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01457-1..10.bam	SRR352936	@dbgap@:reads/SRP020237/SRS405557/SRX101076/SRR352936/SRR352936.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01457_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
04-29264	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01458	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01458	DNA	EFO	SRS405559	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01458 A01458 library	PAIRED	GENOMIC	WGS	RANDOM		A01458	SRX101077	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-04	A01458 A01458 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01458-1..10.bam	SRR352946	@dbgap@:reads/SRP020237/SRS405559/SRX101077/SRR352946/SRR352946.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01458_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-34043	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01459	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01459	DNA	EFO	SRS405560	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01459 A01459 library	PAIRED	GENOMIC	WGS	RANDOM	383	A01459	SRX101078	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-19	A01459 A01459 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01459-1..10.bam	SRR352954	@dbgap@:reads/SRP020237/SRS405560/SRX101078/SRR352954/SRR352954.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01459_A08654_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
07-17613	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01460	organism part	EFO	Solid Tumor	NCIt	"TESTICLE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01460	DNA	EFO	SRS405561	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01460 A01460 library	PAIRED	GENOMIC	WGS	RANDOM		A01460	SRX101079	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-11-19	A01460 A01460 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01460-1..bam	SRR352966	@dbgap@:reads/SRP020237/SRS405561/SRX101079/SRR352966/SRR352966.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01460_A01676_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-30025	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01462	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01462	DNA	EFO	SRS405562	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01462 A01462 library	PAIRED	GENOMIC	WGS	RANDOM		A01462	SRX101080	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-21	A01462 A01462 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01462-1..bam	SRR352970	@dbgap@:reads/SRP020237/SRS405562/SRX101080/SRR352970/SRR352970.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01462_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
07-17613	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01677	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01677	DNA	EFO	SRS405563	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01677 A01677 library	PAIRED	GENOMIC	WGS	RANDOM	360	A01677	SRX101082	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01677 A01677 run	sequencing assay	EFO	199	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01677_9_lanes_dupsFlagged.bam	SRR567560	@dbgap@:reads/SRP020237/SRS405563/SRX101082/SRR567560/SRR567560.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01677_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-24006	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01971	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01971	DNA	EFO	SRS266317	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01971 A01971 library	PAIRED	GENOMIC	WGS	RANDOM		A01971	SRX198286	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A01971 A01971 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A01971_9_lanes_dupsFlagged.bam	SRR598751	@dbgap@:reads/SRP020237/SRS266317/SRX198286/SRR598751/SRR598751.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01971_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-16716	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01972	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01972	DNA	EFO	SRS405564	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01972 A01972 library	PAIRED	GENOMIC	WGS	RANDOM		A01972	SRX101083	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-11	A01972 A01972 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01972-1..bam	SRR352995	@dbgap@:reads/SRP020237/SRS405564/SRX101083/SRR352995/SRR352995.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01972_12_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-16716	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01973	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01973	DNA	EFO	SRS405565	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01973 A01973 library	PAIRED	GENOMIC	WGS	RANDOM		A01973	SRX101084	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-11	A01973 A01973 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01973-1..bam	SRR353007	@dbgap@:reads/SRP020237/SRS405565/SRX101084/SRR353007/SRR353007.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01973_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-24006	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A01974	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01974	DNA	EFO	SRS405566	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A01974 A01974 library	PAIRED	GENOMIC	WGS	RANDOM		A01974	SRX101085	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-10	A01974 A01974 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01974-1..10.bam	SRR353015	@dbgap@:reads/SRP020237/SRS405566/SRX101085/SRR353015/SRR353015.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A01974_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-23907	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A02010	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A02010	DNA	EFO	SRS266321	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A02010 A02010 library	PAIRED	GENOMIC	WGS	RANDOM		A02010	SRX198285	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A02010 A02010 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A02010_9_lanes_dupsFlagged.bam	SRR598753	@dbgap@:reads/SRP020237/SRS266321/SRX198285/SRR598753/SRR598753.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A02010_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-23907	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A02011	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A02011	DNA	EFO	SRS405567	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A02011 A02011 library	PAIRED	GENOMIC	WGS	RANDOM		A02011	SRX101086	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-26	A02011 A02011 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A02011-1..bam	SRR353023	@dbgap@:reads/SRP020237/SRS405567/SRX101086/SRR353023/SRR353023.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A02011_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..fastq	SRR316071	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316071/SRR316071.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..1.fastq	SRR316072	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316072/SRR316072.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..2.fastq	SRR316073	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316073/SRR316073.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..3.fastq	SRR316074	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316074/SRR316074.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..4.fastq	SRR316075	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316075/SRR316075.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..5.fastq	SRR316076	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316076/SRR316076.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..6.fastq	SRR316077	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316077/SRR316077.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03290 A03290 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03290-1..7.fastq	SRR316078	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR316078/SRR316078.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-22	A03290 A03290 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06667-1..fastq	SRR353128	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR353128/SRR353128.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A03290 A03290 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06667-1..1.fastq	SRR353129	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR353129/SRR353129.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A03290 A03290 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06667-1..2.fastq	SRR353130	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR353130/SRR353130.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A03290 A03290 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06667-1..3.fastq	SRR353131	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR353131/SRR353131.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03290	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290	DNA	EFO	SRS405372	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03290 A03290 library	PAIRED	GENOMIC	WGS	RANDOM		A03290	SRX084974	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A03290 A03290 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A03290-bam.bam	SRR390378	@dbgap@:reads/SRP020237/SRS405372/SRX084974/SRR390378/SRR390378.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A03290_A06667_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..1.fastq	SRR316079	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316079/SRR316079.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..2.fastq	SRR316080	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316080/SRR316080.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..3.fastq	SRR316081	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316081/SRR316081.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..4.fastq	SRR316082	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316082/SRR316082.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..5.fastq	SRR316083	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316083/SRR316083.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..6.fastq	SRR316084	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316084/SRR316084.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-28	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..7.fastq	SRR316085	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316085/SRR316085.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-21	A03291 A03291 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	A03291-1..8.fastq	SRR316086	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR316086/SRR316086.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-22	A03291 A03291 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06668-1..fastq	SRR353132	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR353132/SRR353132.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A03291 A03291 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06668-1..1.fastq	SRR353133	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR353133/SRR353133.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A03291 A03291 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06668-1..2.fastq	SRR353134	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR353134/SRR353134.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-13	A03291 A03291 run	sequencing assay	EFO	209	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0	A06668-1..3.fastq	SRR353135	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR353135/SRR353135.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
06-14634	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03291	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291	DNA	EFO	SRS405373	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03291 A03291 library	PAIRED	GENOMIC	WGS	RANDOM		A03291	SRX084975	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	A03291 A03291 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A03291-bam.bam	SRR390379	@dbgap@:reads/SRP020237/SRS405373/SRX084975/SRR390379/SRR390379.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A03291_A06668_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
03-10363	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03561	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03561	DNA	EFO	SRS405568	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03561 A03561 library	PAIRED	GENOMIC	WGS	RANDOM		A03561	SRX101087	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-16	A03561 A03561 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A03561-1..bam	SRR353032	@dbgap@:reads/SRP020237/SRS405568/SRX101087/SRR353032/SRR353032.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A03561_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
03-10363	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A03586	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03586	DNA	EFO	SRS266324	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A03586 A03586 library	PAIRED	GENOMIC	WGS	RANDOM		A03586	SRX198293	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A03586 A03586 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A03586_10_lanes_dupsFlagged.bam	SRR598759	@dbgap@:reads/SRP020237/SRS266324/SRX198293/SRR598759/SRR598759.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A03586_10_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
95-32814	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06417	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06417	DNA	EFO	SRS266325	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06417 A06417 library	PAIRED	GENOMIC	WGS	RANDOM		A06417	SRX198294	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A06417 A06417 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A06417_9_lanes_dupsFlagged.bam	SRR598760	@dbgap@:reads/SRP020237/SRS266325/SRX198294/SRR598760/SRR598760.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A06417_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-24561	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06418	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06418	DNA	EFO	SRS266326	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06418 A06418 library	PAIRED	GENOMIC	WGS	RANDOM	463	A06418	SRX198291	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A06418 A06418 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A08443_A06418_dupsFlagged.bam	SRR598757	@dbgap@:reads/SRP020237/SRS266326/SRX198291/SRR598757/SRR598757.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A08443_A06418_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-12737	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06419	organism part	EFO	Solid Tumor	NCIt	"SPLEEN"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06419	DNA	EFO	SRS405569	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06419 A06419 library	PAIRED	GENOMIC	WGS	RANDOM	383	A06419	SRX101090	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-09	A06419 A06419 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A06419-1..bam	SRR353042	@dbgap@:reads/SRP020237/SRS405569/SRX101090/SRR353042/SRR353042.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A06419_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
95-32814	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06420	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06420	DNA	EFO	SRS405570	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06420 A06420 library	PAIRED	GENOMIC	WGS	RANDOM	424	A06420	SRX101091	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-09	A06420 A06420 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A06420-1..bam	SRR353050	@dbgap@:reads/SRP020237/SRS405570/SRX101091/SRR353050/SRR353050.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A06420_A08655_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
05-24561	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06421	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06421	DNA	EFO	SRS266329	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06421 A06421 library	PAIRED	GENOMIC	WGS	RANDOM	407	A06421	SRX198295	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		A06421 A06421 run	sequencing assay	EFO	197	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A08444_A06421_dupsFlagged.bam	SRR598762	@dbgap@:reads/SRP020237/SRS266329/SRX198295/SRR598762/SRR598762.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A08444_A06421_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-12737	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06422	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06422	DNA	EFO	SRS405571	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06422 A06422 library	PAIRED	GENOMIC	WGS	RANDOM		A06422	SRX101092	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-09	A06422 A06422 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A06422-1..bam	SRR353058	@dbgap@:reads/SRP020237/SRS405571/SRX101092/SRR353058/SRR353058.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A06422_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
07-30628	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06720	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06720	DNA	EFO	SRS405572	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06720 A06720 library	PAIRED	GENOMIC	WGS	RANDOM		A06720	SRX101093	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-29	A06720 A06720 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A06720-1..bam	SRR353066	@dbgap@:reads/SRP020237/SRS405572/SRX101093/SRR353066/SRR353066.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A06720_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
07-30628	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	A06721	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06721	DNA	EFO	SRS405573	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	A06721 A06721 library	PAIRED	GENOMIC	WGS	RANDOM		A06721	SRX101094	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-06-29	A06721 A06721 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.36.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A06721-1..bam	SRR353074	@dbgap@:reads/SRP020237/SRS405573/SRX101094/SRR353074/SRR353074.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	A06721_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_1	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_1	DNA	EFO	SRS591655	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_1 A12437 library	PAIRED	GENOMIC	WGS	RANDOM		A12437	SRX516277	"WGS analysis of diffuse large B-cell lymphoma cell line DB[P6] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_1 A12437 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A12437_3_lanes_dupsFlagged.bam	SRR1236468	@dbgap@:reads/SRP020237/SRS591655/SRX516277/SRR1236468/SRR1236468.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_2	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_2	DNA	EFO	SRS591656	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_2 A12438 library	PAIRED	GENOMIC	WGS	RANDOM		A12438	SRX516275	"WGS analysis of diffuse large B-cell lymphoma cell line DoHH-2[P9] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_2 A12438 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12438_3_lanes_dupsFlagged.bam	SRR1236474	@dbgap@:reads/SRP020237/SRS591656/SRX516275/SRR1236474/SRR1236474.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_3	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_3	DNA	EFO	SRS591657	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_3 A12439 library	PAIRED	GENOMIC	WGS	RANDOM		A12439	SRX516274	"WGS analysis of diffuse large B-cell lymphoma cell line Karpas 422[P8] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_3 A12439 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A12439_3_lanes_dupsFlagged.bam	SRR1236478	@dbgap@:reads/SRP020237/SRS591657/SRX516274/SRR1236478/SRR1236478.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_4	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_4	DNA	EFO	SRS591658	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_4 A12440 library	PAIRED	GENOMIC	WGS	RANDOM		A12440	SRX516278	"WGS analysis of diffuse large B-cell lymphoma cell line MD903[P7] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_4 A12440 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12440_3_lanes_dupsFlagged.bam	SRR1236472	@dbgap@:reads/SRP020237/SRS591658/SRX516278/SRR1236472/SRR1236472.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_5	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_5	DNA	EFO	SRS591659	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_5 A12441 library	PAIRED	GENOMIC	WGS	RANDOM		A12441	SRX516270	"WGS analysis of diffuse large B-cell lymphoma cell line NU-DHL-1[P11] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_5 A12441 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12441_3_lanes_dupsFlagged.bam	SRR1236467	@dbgap@:reads/SRP020237/SRS591659/SRX516270/SRR1236467/SRR1236467.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_6	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_6	DNA	EFO	SRS591660	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_6 A12442 library	PAIRED	GENOMIC	WGS	RANDOM		A12442	SRX516273	"WGS analysis of diffuse large B-cell lymphoma cell line NU-DUL-1[P9] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_6 A12442 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12442_3_lanes_dupsFlagged.bam	SRR1236469	@dbgap@:reads/SRP020237/SRS591660/SRX516273/SRR1236469/SRR1236469.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_7	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_7	DNA	EFO	SRS591661	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_7 A12443 library	PAIRED	GENOMIC	WGS	RANDOM		A12443	SRX516279	"WGS analysis of diffuse large B-cell lymphoma cell line OCI-Ly1[P8] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_7 A12443 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12443_3_lanes_dupsFlagged.bam	SRR1236466	@dbgap@:reads/SRP020237/SRS591661/SRX516279/SRR1236466/SRR1236466.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_8	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_8	DNA	EFO	SRS591662	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_8 A12444 library	PAIRED	GENOMIC	WGS	RANDOM		A12444	SRX516269	"WGS analysis of diffuse large B-cell lymphoma cell line OCI-Ly7[P8] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_8 A12444 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	A12444_3_lanes_dupsFlagged.bam	SRR1236470	@dbgap@:reads/SRP020237/SRS591662/SRX516269/SRR1236470/SRR1236470.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_9	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_9	DNA	EFO	SRS591663	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_9 A12445 library	PAIRED	GENOMIC	WGS	RANDOM		A12445	SRX516272	"WGS analysis of diffuse large B-cell lymphoma cell line OCI-Ly19[P9] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_9 A12445 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12445_3_lanes_dupsFlagged.bam	SRR1236477	@dbgap@:reads/SRP020237/SRS591663/SRX516272/SRR1236477/SRR1236477.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_10	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_10	DNA	EFO	SRS591664	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_10 A12446 library	PAIRED	GENOMIC	WGS	RANDOM		A12446	SRX516268	"WGS analysis of diffuse large B-cell lymphoma cell line SU-DHL-6[P8] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_10 A12446 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12446_3_lanes_dupsFlagged.bam	SRR1236476	@dbgap@:reads/SRP020237/SRS591664/SRX516268/SRR1236476/SRR1236476.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_11	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_11	DNA	EFO	SRS591665	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_11 A12447 library	PAIRED	GENOMIC	WGS	RANDOM		A12447	SRX516276	"WGS analysis of diffuse large B-cell lymphoma cell line SU-DHL-9[P7] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_11 A12447 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12447_3_lanes_dupsFlagged.bam	SRR1236473	@dbgap@:reads/SRP020237/SRS591665/SRX516276/SRR1236473/SRR1236473.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_12	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_12	DNA	EFO	SRS591666	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_12 A14217 library	PAIRED	GENOMIC	WGS	RANDOM	427	A14217	SRX516267	"WGS analysis of diffuse large B-cell lymphoma cell line WSU-DLCL2[P6] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-03-14	AM_12 A14217 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A14217_3_lanes_dupsFlagged.bam	SRR1236475	@dbgap@:reads/SRP020237/SRS591666/SRX516267/SRR1236475/SRR1236475.sra	2	NCBI36_BCCAGSC_variant			
	Children's Oncology Group	whole organism	EFO		NCBITaxon		NCIt	Diffuse Large B-Cell Lymphoma	NCIt	AM_13	cell line	EFO	Cell Line	NCIt	""	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_13	DNA	EFO	SRS591667	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	AM_13 A12449 library	PAIRED	GENOMIC	WGS	RANDOM		A12449	SRX516271	"WGS analysis of diffuse large B-cell lymphoma cell line OCI-Ly3[P10] using Illumina HiSeq 2000"	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2012-01-13	AM_13 A12449 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2					bcgsc.ca:Protocol:WGS-ReadAlign:01	A12449_3_lanes_dupsFlagged.bam	SRR1236471	@dbgap@:reads/SRP020237/SRS591667/SRX516271/SRR1236471/SRR1236471.sra	2	NCBI36_BCCAGSC_variant			
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2008-11-26	HS0733 HS0733 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..fastq	SRR316087	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316087/SRR316087.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..1.fastq	SRR316088	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316088/SRR316088.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..2.fastq	SRR316089	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316089/SRR316089.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..3.fastq	SRR316090	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316090/SRR316090.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..4.fastq	SRR316091	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316091/SRR316091.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..5.fastq	SRR316092	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316092/SRR316092.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..6.fastq	SRR316093	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316093/SRR316093.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-06	HS0733 HS0733 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0733-1..7.fastq	SRR316094	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR316094/SRR316094.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt		NCIt	HS0733	organism part	EFO		NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733	DNA	EFO	SRS405381	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0733 HS0733 library	PAIRED	GENOMIC	WGS	RANDOM	190	HS0733	SRX084976	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2010-10-22	HS0733 HS0733 run	sequencing assay	EFO	98	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS0733-bam.bam	SRR390362	@dbgap@:reads/SRP020237/SRS405381/SRX084976/SRR390362/SRR390362.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS0733_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2008-11-25	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..fastq	SRR316095	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316095/SRR316095.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..1.fastq	SRR316096	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316096/SRR316096.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..10.fastq	SRR316097	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316097/SRR316097.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..11.fastq	SRR316098	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316098/SRR316098.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..12.fastq	SRR316099	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316099/SRR316099.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..13.fastq	SRR316100	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316100/SRR316100.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..2.fastq	SRR316101	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316101/SRR316101.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..3.fastq	SRR316102	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316102/SRR316102.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..4.fastq	SRR316103	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316103/SRR316103.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..5.fastq	SRR316104	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316104/SRR316104.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..6.fastq	SRR316105	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316105/SRR316105.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-05	HS0821 HS0821 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..7.fastq	SRR316106	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316106/SRR316106.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..8.fastq	SRR316107	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316107/SRR316107.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0821 HS0821 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS0821-1..9.fastq	SRR316108	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR316108/SRR316108.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0821	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821	DNA	EFO	SRS405465	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0821 HS0821 library	PAIRED	GENOMIC	WGS	RANDOM	353	HS0821	SRX084977	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2010-10-22	HS0821 HS0821 run	sequencing assay	EFO	88	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS0821-bam.bam	SRR390365	@dbgap@:reads/SRP020237/SRS405465/SRX084977/SRR390365/SRR390365.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS0821_14_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2008-12-15	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..fastq	SRR036297	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036297/SRR036297.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..1.fastq	SRR036298	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036298/SRR036298.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..10.fastq	SRR036299	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036299/SRR036299.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..11.fastq	SRR036300	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036300/SRR036300.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..12.fastq	SRR036301	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036301/SRR036301.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..13.fastq	SRR036302	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036302/SRR036302.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..14.fastq	SRR036303	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036303/SRR036303.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..15.fastq	SRR036304	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036304/SRR036304.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..16.fastq	SRR036305	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036305/SRR036305.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..17.fastq	SRR036306	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036306/SRR036306.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..18.fastq	SRR036307	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036307/SRR036307.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..19.fastq	SRR036308	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036308/SRR036308.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..2.fastq	SRR036309	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036309/SRR036309.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-30	HS0896 HS0896 run	sequencing assay	EFO	95	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..20.fastq	SRR036310	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036310/SRR036310.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..21.fastq	SRR036311	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036311/SRR036311.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..22.fastq	SRR036312	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036312/SRR036312.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..23.fastq	SRR036313	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036313/SRR036313.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..24.fastq	SRR036314	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036314/SRR036314.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..25.fastq	SRR036315	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036315/SRR036315.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..26.fastq	SRR036316	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036316/SRR036316.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..27.fastq	SRR036317	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036317/SRR036317.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-05	HS0896 HS0896 run	sequencing assay	EFO	100	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..28.fastq	SRR036318	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036318/SRR036318.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-20	HS0896 HS0896 run	sequencing assay	EFO	152	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..29.fastq	SRR036319	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036319/SRR036319.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..3.fastq	SRR036320	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036320/SRR036320.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-20	HS0896 HS0896 run	sequencing assay	EFO	152	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..30.fastq	SRR036321	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036321/SRR036321.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-20	HS0896 HS0896 run	sequencing assay	EFO	152	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..31.fastq	SRR036322	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036322/SRR036322.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-20	HS0896 HS0896 run	sequencing assay	EFO	152	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..32.fastq	SRR036323	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036323/SRR036323.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-20	HS0896 HS0896 run	sequencing assay	EFO	152	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..33.fastq	SRR036324	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036324/SRR036324.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-02-20	HS0896 HS0896 run	sequencing assay	EFO	152	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..34.fastq	SRR036325	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036325/SRR036325.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-12	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..4.fastq	SRR036326	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036326/SRR036326.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..5.fastq	SRR036327	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036327/SRR036327.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..6.fastq	SRR036328	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036328/SRR036328.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..7.fastq	SRR036329	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036329/SRR036329.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..8.fastq	SRR036330	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036330/SRR036330.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA	2009-01-22	HS0896 HS0896 run	sequencing assay	EFO	72	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5	HS08961..9.fastq	SRR036331	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR036331/SRR036331.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
06-12968	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Follicular Lymphoma	NCIt	HS0896	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896	DNA	EFO	SRS405609	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS0896 HS0896 library	PAIRED	GENOMIC	WGS	RANDOM		HS0896	SRX016866	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	BCCA		HS0896 HS0896 run	sequencing assay	EFO	98	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.5					bcgsc.ca:Protocol:WGS-ReadAlign:01	HS08961-bam.bam	SRR390736	@dbgap@:reads/SRP020237/SRS405609/SRX016866/SRR390736/SRR390736.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS0896_35_lanes_dupsFlagged.bam.varFilter.0.1.12a.snps.anno.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..fastq	SRR316109	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316109/SRR316109.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..1.fastq	SRR316110	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316110/SRR316110.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..2.fastq	SRR316111	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316111/SRR316111.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..3.fastq	SRR316112	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316112/SRR316112.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..4.fastq	SRR316113	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316113/SRR316113.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..5.fastq	SRR316114	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316114/SRR316114.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..6.fastq	SRR316115	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316115/SRR316115.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2702 HS2702 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2702-1..7.fastq	SRR316116	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR316116/SRR316116.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2702	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702	DNA	EFO	SRS405374	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2702 HS2702 library	PAIRED	GENOMIC	WGS	RANDOM	394	HS2702	SRX084978	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	HS2702 HS2702 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2702-bam.bam	SRR390366	@dbgap@:reads/SRP020237/SRS405374/SRX084978/SRR390366/SRR390366.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2702_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..fastq	SRR316117	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316117/SRR316117.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..1.fastq	SRR316118	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316118/SRR316118.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..2.fastq	SRR316119	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316119/SRR316119.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..3.fastq	SRR316120	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316120/SRR316120.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..4.fastq	SRR316121	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316121/SRR316121.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..5.fastq	SRR316122	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316122/SRR316122.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..6.fastq	SRR316123	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316123/SRR316123.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-08-17	HS2703 HS2703 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2703-1..7.fastq	SRR316124	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR316124/SRR316124.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
98-22532	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2703	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703	DNA	EFO	SRS405375	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2703 HS2703 library	PAIRED	GENOMIC	WGS	RANDOM	386	HS2703	SRX084979	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	HS2703 HS2703 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2703-bam.bam	SRR390367	@dbgap@:reads/SRP020237/SRS405375/SRX084979/SRR390367/SRR390367.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2703_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
07-35482	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2704	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2704	DNA	EFO	SRS405574	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2704 HS2704 library	PAIRED	GENOMIC	WGS	RANDOM	405	HS2704	SRX101097	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-10	HS2704 HS2704 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2704-1..12.bam	SRR353084	@dbgap@:reads/SRP020237/SRS405574/SRX101097/SRR353084/SRR353084.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2704_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
07-35482	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2705	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2705	DNA	EFO	SRS405575	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2705 HS2705 library	PAIRED	GENOMIC	WGS	RANDOM	390	HS2705	SRX101098	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-01-10	HS2705 HS2705 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2705-1..12.bam	SRR353092	@dbgap@:reads/SRP020237/SRS405575/SRX101098/SRR353092/SRR353092.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2705_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..fastq	SRR316125	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316125/SRR316125.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..1.fastq	SRR316126	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316126/SRR316126.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..2.fastq	SRR316127	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316127/SRR316127.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..3.fastq	SRR316128	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316128/SRR316128.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..4.fastq	SRR316129	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316129/SRR316129.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..5.fastq	SRR316130	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316130/SRR316130.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..6.fastq	SRR316131	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316131/SRR316131.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2706 HS2706 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2706-1..7.fastq	SRR316132	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR316132/SRR316132.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2706	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706	DNA	EFO	SRS405376	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2706 HS2706 library	PAIRED	GENOMIC	WGS	RANDOM	407	HS2706	SRX084980	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	HS2706 HS2706 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2706-bam.bam	SRR390380	@dbgap@:reads/SRP020237/SRS405376/SRX084980/SRR390380/SRR390380.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2706_8_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..fastq	SRR316133	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316133/SRR316133.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..1.fastq	SRR316134	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316134/SRR316134.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..2.fastq	SRR316135	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316135/SRR316135.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..3.fastq	SRR316136	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316136/SRR316136.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..4.fastq	SRR316137	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316137/SRR316137.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..5.fastq	SRR316138	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316138/SRR316138.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..6.fastq	SRR316139	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316139/SRR316139.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-07	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2707-1..7.fastq	SRR316140	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR316140/SRR316140.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-07-19	HS2707 HS2707 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.12.4.2	HS2707-1..8.fastq	SRR363383	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR363383/SRR363383.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
05-23110	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2707	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707	DNA	EFO	SRS405377	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2707 HS2707 library	PAIRED	GENOMIC	WGS	RANDOM	387	HS2707	SRX084981	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	HS2707 HS2707 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2707-bam.bam	SRR390381	@dbgap@:reads/SRP020237/SRS405377/SRX084981/SRR390381/SRR390381.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2707_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
02-22991	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2970	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2970	DNA	EFO	SRS405576	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2970 HS2970 library	PAIRED	GENOMIC	WGS	RANDOM		HS2970	SRX101099	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-02-08	HS2970 HS2970 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2970-1..bam	SRR353101	@dbgap@:reads/SRP020237/SRS405576/SRX101099/SRR353101/SRR353101.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2970_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
02-22991	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2971	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2971	DNA	EFO	SRS266336	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2971 HS2971 library	PAIRED	GENOMIC	WGS	RANDOM		HS2971	SRX198298	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		HS2971 HS2971 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2971_9_lanes.bam	SRR598764	@dbgap@:reads/SRP020237/SRS266336/SRX198298/SRR598764/SRR598764.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2971_9_lanes_dupsFlagged.varFilter.anno1.maf.txt	3
08-15460	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2972	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2972	DNA	EFO	SRS266337	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2972 HS2972 library	PAIRED	GENOMIC	WGS	RANDOM	517	HS2972	SRX198288	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA		HS2972 HS2972 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2972_A01126_dupsFlagged.bam	SRR598754	@dbgap@:reads/SRP020237/SRS266337/SRX198288/SRR598754/SRR598754.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2972_A01126_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
08-15460	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	female	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2973	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2973	DNA	EFO	SRS405577	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2973 HS2973 library	PAIRED	GENOMIC	WGS	RANDOM		HS2973	SRX101100	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2973 HS2973 run	sequencing assay	EFO	200	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0					bcgsc.ca:Protocol:WGS-ReadAlign:01	A01127-1..bam	SRR352729	@dbgap@:reads/SRP020237/SRS405577/SRX101100/SRR352729/SRR352729.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2973_A01127_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..fastq	SRR316141	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316141/SRR316141.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..1.fastq	SRR316142	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316142/SRR316142.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..2.fastq	SRR316143	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316143/SRR316143.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..3.fastq	SRR316144	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316144/SRR316144.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..4.fastq	SRR316145	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316145/SRR316145.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..5.fastq	SRR316146	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316146/SRR316146.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2974-1..6.fastq	SRR316147	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316147/SRR316147.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-03-25	HS2974 HS2974 run	sequencing assay	EFO	50	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.1	HS2974-1..7.fastq	SRR316148	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316148/SRR316148.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-04-06	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Bustard 1.9.0	HS2974-1..9.fastq	SRR316149	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR316149/SRR316149.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2974 HS2974 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0	A01128-1..fastq	SRR353118	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR353118/SRR353118.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2974	organism part	EFO	Solid Tumor	NCIt	"LYMPH NODE"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974	DNA	EFO	SRS405378	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2974 HS2974 library	PAIRED	GENOMIC	WGS	RANDOM	455	HS2974	SRX084982	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	HS2974 HS2974 run	sequencing assay	EFO	172	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2974-bam.bam	SRR390382	@dbgap@:reads/SRP020237/SRS405378/SRX084982/SRR390382/SRR390382.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2974_A01128_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..fastq	SRR316150	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316150/SRR316150.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..1.fastq	SRR316151	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316151/SRR316151.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-04-06	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.1	HS2975-1..10.fastq	SRR316152	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316152/SRR316152.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..2.fastq	SRR316153	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316153/SRR316153.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-09-27	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..3.fastq	SRR316154	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316154/SRR316154.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..4.fastq	SRR316155	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316155/SRR316155.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..5.fastq	SRR316156	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316156/SRR316156.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.0	HS2975-1..6.fastq	SRR316157	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316157/SRR316157.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2011-03-25	HS2975 HS2975 run	sequencing assay	EFO	50	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.10.1	HS2975-1..7.fastq	SRR316158	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR316158/SRR316158.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-07	HS2975 HS2975 run	sequencing assay	EFO	202	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	Illumina RTA 1.7.48.0	A01129-1..fastq	SRR353119	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR353119/SRR353119.sra	1							bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
09-33003	Children's Oncology Group	whole organism	EFO	Homo sapiens	NCBITaxon	male	NCIt	Diffuse Large B-Cell Lymphoma	NCIt	HS2975	organism part	EFO	Normal Tissue	NCIt	"PERIPHERAL BLOOD"	bcgsc.ca:Protocol:DNA-Extraction:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975	DNA	EFO	SRS405379	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	BC Cancer Agency Michael Smith Genome Sciences Centre	HS2975 HS2975 library	PAIRED	GENOMIC	WGS	RANDOM		HS2975	SRX084983	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	BCCA	2010-10-22	HS2975 HS2975 run	sequencing assay	EFO	176	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01						bcgsc.ca:Protocol:WGS-ReadAlign:01	HS2975-bam.bam	SRR390383	@dbgap@:reads/SRP020237/SRS405379/SRX084983/SRR390383/SRR390383.sra	2	NCBI36_BCCAGSC_variant	bcgsc.ca:Protocol:WGS-VariantCall:01	HS2975_A01129_dupsFlagged.pileup.varFilter.anno1.maf.txt	3
