MAGE-TAB Version	1.1
Investigation Title	CGCI: Non-Hodgkin Lymphoma (NHL) WXS
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:WXS-LibraryPrep-Illumina:01	bcgsc.ca:Protocol:WXS-ExomeCapture-Illumina:01	bcgsc.ca:Protocol:WXS-Sequence-Illumina-GAIIx:01	bcgsc.ca:Protocol:WXS-BaseCall-Illumina:01	bcgsc.ca:Protocol:WXS-ReadAlign:01	bcgsc.ca:Protocol:WXS-VariantCall:01
Protocol Type	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid library construction 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							
Protocol Parameters					Software Versions		
Protocol Hardware				Illumina Genome Analyzer IIx			
Protocol Software					Bustard;Illumina RTA		
Protocol Contact
SDRF File	CGCI_NHL_WXS_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
