MAGE-TAB Version	1.1
Investigation Title	CGCI: Non-Hodgkin Lymphoma (NHL) WGS
Experimental Design	disease state design
Experimental Design Term Source REF	EFO
Experimental Factor Name
Experimental Factor Type
Experimental Factor Term Source REF
Person Last Name	NCI Office of Cancer Genomics (OCG)	NCI Center for Biomedical Informatics and Information Technology (CBIIT)
Person First Name		
Person Mid Initials		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov
Person Phone	+1 301 451 8027	+1 888 478 4423
Person Fax	+1 301 480 4368	
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850
Person Affiliation	National Cancer Institute	National Cancer Institute
Person Roles	funder	data coder;curator
Person Roles Term Source REF	EFO	EFO;EFO
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date
PubMed ID
Publication DOI
Publication Author List
Publication Title
Publication Status
Publication Status Term Source REF
Experiment Description	"The Office of Cancer Genomics (OCG) at the National Cancer Institute is sponsoring a series of studies as part of the Cancer Genome Characterization Initiative (CGCI) to assess novel emerging sequencing technologies in cancer. The CGCI program includes comprehensive characterization of the genetic aberrations found in different pediatric and/or adult tumors. CGCI is currently characterizing a number of B-cell non-Hodgkin lymphomas (including diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and adult and pediatric Burkitt lymphomas). In combination, the lymphoid cancers (non-Hodgkin lymphoma, Hodgkin lymphoma, myeloma and chronic lymphocytic leukemia), constitute the fourth most common malignancy in both men and women in North America. Lymphomas typically have characteristic abnormal chromosomes, including translocations, indicating the relevance of mutations to how NHLs develop and behave. This project uses detailed analysis on a specific... (for more see dbGaP study page.)"
Protocol Name	bcgsc.ca:Protocol:DNA-Extraction:01	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	bcgsc.ca:Protocol:WGS-Sequence-Illumina-GAIIx:01	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	bcgsc.ca:Protocol:WGS-ReadAlign:01	bcgsc.ca:Protocol:WGS-VariantCall:01
Protocol Type	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	nucleic acid sequencing protocol	data transformation protocol	data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description		"DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was subsequently diluted to 10nM. The final concentration was confirmed using a Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen, Carlsbad, CA, USA)."				"Illumina paired-end whole genome sequencing reads were aligned to the hg19 reference using BWA version 0.5.7. This reference contains chromosomes 1-22, X, Y, MT, 20 unlocalized scaffolds and 39 unplaced scaffolds. Multiple lanes of sequences were merged and duplicated reads were marked with Picard Tools."	
Protocol Parameters					Software Versions		
Protocol Hardware			Illumina Genome Analyzer IIx	Illumina HiSeq 2000			
Protocol Software					Bustard;Illumina RTA		
Protocol Contact
SDRF File	CGCI_NHL_WGS_20160906.sdrf.txt
Term Source Name	NCBITaxon	NCIt	MO	EFO	OBI
Term Source File	http://www.ncbi.nlm.nih.gov/taxonomy	http://ncit.nci.nih.gov/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo	http://purl.obolibrary.org/obo/obi
Term Source Version
Comment[SRA_STUDY]	SRP020237
Comment[BioProject]	PRJNA172563
Comment[dbGaP Study]	phs000532
