MAGE-TAB Version	1.1
Investigation Title	TARGET: Kidney - Clear Cell Sarcoma of the Kidney (CCSK) 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)	Gadd	Perlman
Person First Name			Samantha	Elizabeth
Person Mid Initials			L	J
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	sgadd@luriechildrens.org	eperlman@luriechildrens.org
Person Phone	+1 301 451 8027	+1 888 478 4423	+1 773 755 6392	+1 312 227 3967
Person Fax	+1 301 480 4368			
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	2430 N Halsted St, Room C366 Chicago, IL 60614	225 E Chicago Ave, Chicago, IL 60611
Person Affiliation	National Cancer Institute	National Cancer Institute	Lurie Children's Hospital of Chicago Research Center	Ann & Robert H. Lurie Children's Hospital of Chicago
Person Roles	funder;investigator	data coder;curator	investigator;data analyst	investigator
Person Roles Term Source REF	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 (CCSK) and rhabdoid tumor. CCSK is a rare, aggressive kidney tumor that usually occurs in children younger than 3 years of age and little is known about the biology of this disease. There are 13 patient cases in the CCSK dataset, each with gene expression, methylation and comprehensive next-generation sequencing to include whole genome sequencing of tumor/normal pairs and mRNA-seq. 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 on this and other TARGET genomics projects. Please see the TARGET Publication... (for more see dbGaP study page.)"
Protocol Name	nationwidechildrens.org:Protocol:DNA-Extraction-Qiagen-AllPrep:01	completegenomics.com:Protocol:WGS-LibraryPrep-CGI:01	completegenomics.com:Protocol:WGS-Sequence-CGI-CGI:01	completegenomics.com:Protocol:WGS-BaseCall-CGI:01	completegenomics.com:Protocol:WGS-ReadAlign-CGI:01	completegenomics.com:Protocol:WGS-Circos-CGI:01	completegenomics.com:Protocol:WGS-CnvSegment-CGI:01	completegenomics.com:Protocol:WGS-FilterSomatic-CGI:01	completegenomics.com:Protocol:WGS-VariantCall-CGI:01	completegenomics.com:Protocol:WGS-HigherLevelSummary-CGI:01	completegenomics.com:Protocol:WGS-Junction-CGI:01	completegenomics.com:Protocol:WGS-Vcf2Maf-CGI:01
Protocol Type	nucleic acid extraction protocol	nucleic acid library construction 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	data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	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."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."	"Complete Genomics Inc. standard protocol, please see CGI READMEs for details."
Protocol Parameters												
Protocol Hardware			Complete Genomics									
Protocol Software												
Protocol Contact
SDRF File	TARGET_CCSK_WGS_20170609.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]	SRP012001
Comment[BioProject]	PRJNA89537
Comment[dbGaP Study]	phs000466
