MAGE-TAB Version	1.1
Investigation Title	TARGET: Kidney - Rhabdoid Tumor (RT) 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)	Perlman	Ma	Novik
Person First Name			Elizabeth	Yussanne	Karen
Person Mid Initials				P	L
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	eperlman@luriechildrens.org	yma@bcgsc.ca	knovik@bcgsc.ca
Person Phone	+1 301 451 8027	+1 888 478 4423	+1 312 227 3967	+1 604 707 5800 Ext 6082	+1 604 707 8000 Ext 7983
Person Fax	+1 301 480 4368			+1 604 876 3561	+1 604 675 8178
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	225 E Chicago Ave, Chicago, IL 60611	Suite 100-570 West 7th Ave, Vancouver, BC Canada V5Z 4S6	675 West 10th Ave Vancouver, BC Canada V5Z 1L3
Person Affiliation	National Cancer Institute	National Cancer Institute	Ann & Robert H. Lurie Children's Hospital of Chicago	BC Cancer Agency Canada's Michael Smith Genome Sciences Centre	BC Cancer Agency Canada's Michael Smith Genome Sciences Centre
Person Roles	funder;investigator	data coder;curator	investigator	investigator;data analyst;submitter	investigator
Person Roles Term Source REF	EFO;EFO	EFO;EFO	EFO	EFO;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	"To further explore some more aggressive subtypes in pediatric cancer already under study in OCG, CGCI is partnering with TARGET initiative to support extensive sequencing analysis of three hard to treat childhood cancers: refractory to treatment cases of acute myeloid leukemia and two rare kidney tumors; clear cell sarcoma of the kidney and rhabdoid tumor (RT). Rhabdoid tumors are a rare, very aggressive type of kidney tumor of infancy, and patients typically have a poor prognosis. Up to 40 patient cases of matched tumor and normal samples, as well as some established cell lines, will undergo whole genome sequencing, miRNA-seq and mRNA-seq, DNA methyl-seq and ChIP-seq to generate a comprehensive profile and hopefully facilitate the development of better therapeutic options for this tumor subtype. All cases can be sorted according to data type via the Case Matrix on the TARGET Data Matrix. Please visit the TARGET website listed above for additional information... (for more see dbGaP study page.)"
Protocol Name	nationwidechildrens.org:Protocol:DNA-Extraction-Qiagen-AllPrep:01	bcgsc.ca:Protocol:WGS-LibraryPrep-Illumina:01	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2000:01	bcgsc.ca:Protocol:WGS-Sequence-Illumina-HiSeq2500:01	bcgsc.ca:Protocol:WGS-BaseCall-Illumina:01	bcgsc.ca:Protocol:WGS-ReadAlign-BWA-Picard:01	bcgsc.ca:Protocol:WGS-VariantCall-Mpileup:01	bcgsc.ca:Protocol:WGS-StructVariant-ABySS:01	bcgsc.ca:Protocol:WGS-VariantCall-Strelka:01	bcgsc.ca:Protocol:WGS-Mpileup-Vcf2Maf:01	bcgsc.ca:Protocol:WGS-Strelka-Vcf2Maf: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	data transformation protocol	data transformation protocol	data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"Genomic DNA was prepared from using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). Please see https://ocg.cancer.gov/programs/target/target-methods for full extraction protocol details."	"Genomic DNA for construction of whole genome shotgun sequencing (WGSS) libraries was prepared from the same biopsy material using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA quality was assessed by spectrophotometry (260/280 and 260/230) and gel electrophoresis before library construction. Depending on the availability of DNA, between 2 and 10ug was used in WGSS library construction. Briefly, DNA was sheared for 10 min using a Sonic Dismembrator 550 with a power setting of "7" in pulses of 30 seconds interspersed with 30 seconds of cooling (Cup Horn, Fisher Scientific, Ottawa, Ontario, Canada), and analyzed on 8% PAGE gels. The 200-300bp DNA fraction was excised and eluted from the gel slice overnight at 4 degrees Celsius in 300 ul of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. WGSS libraries were prepared using a modified paired-end protocol supplied by Illumina Inc. (Illumina, Hayward, USA). This involved DNA end-repair and formation of 3' A overhangs using Klenow fragment (3' to 5' exo minus) and ligation to Illumina PE adapters (with 5' overhangs). Adapter-ligated products were purified on Qiaquick spin columns (Qiagen, Valencia, CA, USA) and PCR-amplified using Phusion DNA polymerase (NEB, Ipswich, MA, USA) and 10 cycles with the PE primer 1.0 and 2.0 (Illumina). PCR products of the desired size range were purified from adapter ligation artifacts using 8% PAGE gels. DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent, Santa Clara CA, USA) and Nanodrop 7500 spectrophotometer (Nanodrop, Wilmington, DE, USA) and DNA was 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."	"SNVs were analyzed with SAMtools mpileup v.0.1.17 (Li et al., 2009) either on single or paired libraries. Each chromosome was analyzed separately using the -C50-DSBuf parameters. The resulting vcf files were merged and filtered to remove low quality SNVs by using samtools varFilter (with default parameters) as well as to remove SNVs with a QUAL score of less than 20 (vcf column 6). Finally, SNVs were annotated with gene annotations from ensembl v66 using snpEff (Cingolani et al., 2012b) and the dbSNP v137 db membership assigned using snpSift (Cingolani et al., 2012a)."	"Structural variant detection was performed using ABySS (v1.3.2). Genome (WGS) libraries were assembled in single end mode using k-mer values of k24 and k44. The contigs and reads were then reassembled at k64 in single end mode and then finally at k64 in paired end mode. The meta-assemblies were then used as input to the Trans-ABySS analysis pipeline (Robertson et al., 2010). Large scale rearrangements and gene fusions from RNA-seq libraries were identified from contigs that had high confidence GMAP (v2012-12-20) alignments to two distinct genomic regions. Evidence for the alignments were provided from aligning reads back to the contigs and from aligning reads to genomic coordinates. Events were then filtered on read thresholds. Large scale rearrangements and gene fusions from WGS libraries were identified in a similar way, but using BWA (v0.6.2-r126) alignments. Insertions and deletions were identified by gapped alignment of contigs to the human reference using GMAP for RNA-seq and BWA for WGS. Confidence in the event was calculated from the alignment of reads back to the event breakpoint in the contigs. The events were then screened against dbSNP and other variation databases to identify putative novel events. To determine compartment specific events the structural variant calls for each patient from all matched genome and RNA-seq samples were concatenated together and screened against matching genome tumour, and where available germline bam files. This resulted in compartment specific structural variant events and where germline was available putative somatic and germline events. The events were further filtered against a compendium of germline structural variants to remove recurrent false positives."	"To analyze compartment specific SNVs, samples were analyzed pair wise with the default settings of Strelka v0.4.7 (Saunders et al., 2012). Primary tumor samples and relapse/met were compared against the germline sample. In the absence of a germline sample, the relapse/met samples were compared against the primary tumor sample."		
Protocol Parameters					Software Versions						
Protocol Hardware			Illumina HiSeq 2000	Illumina HiSeq 2500							
Protocol Software					Illumina RTA						
Protocol Contact
SDRF File	TARGET_RT_WGS_20190320.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]	SRP012005
Comment[BioProject]	PRJNA89539
Comment[dbGaP Study]	phs000470
