MAGE-TAB Version	1.1					
Investigation Title	TARGET Project SNP Array Profiling of DNA Copy Number Alterations in the Children’s Oncology Group P9906 Cohort					
Experimental Design	genotyping design	disease state design				
Experimental Design Term Source REF	EFO	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)	Song	Mullighan	Hunger	
Person First Name			Guangchun	Charles	Stephen	
Person Mid Initials					P	
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	guangchun.song@stjude.org	charles.mullighan@stjude.org	hungers@chop.edu	
Person Phone	+1 301 451 8027	+1 888 478 4423		901-595-3387		
Person Fax	+1 301 480 4368			901-595-5947		
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850		262 Danny Thomas Place, Mail Stop 342, Memphis TN 38105	3401 Civic Center Blvd Philadelphia, PA 19104	
Person Affiliation	National Cancer Institute	National Cancer Institute	St Jude Children’s Research Hospital	St Jude Children’s Research Hospital	Children's Hospital of Philadelphia	
Person Roles	funder	data coder;curator	data analyst;submitter	investigator	investigator	
Person Roles Term Source REF	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						
Protocol Name	stjude.org:Protocol:DNA-Extraction:01	stjude.org:Protocol:CopyNumberArray-Labeling-Affymetrix-250k:01	stjude.org:Protocol:CopyNumberArray-Hybridization-Affymetrix-250k:01	stjude.org:Protocol:CopyNumberArray-Scanning-Affymetrix-250k:01	stjude.org:Protocol:CopyNumberArray-DataNormalization-GTYPE:01	stjude.org:Protocol:CopyNumberArray-CnvSegment:01
Protocol Type	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol 	array scanning protocol	normalization data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	""	"Affymetrix Mapping 250k labeling protocol"	"Affymetrix Mapping 250k hybridization protocol"	"Affymetrix Mapping 250k scanning protocol"	"250K genotypes were generated using the BRLMM algorithm implemented in GTYPE (Affymetrix).  SNP6 genotypes were generated using the birdseed v2 algorithm in Genotyping Console (Affymetrix). Samples that failed standard QC metrics (contrast QC) were excluded.  To generate copy number data, data were analyzed using a extensively used and validated algorithm developed at St Jude Children’s Research Hospital.  Affymetrix SNP array CEL files and SNP call files (either .CHP or .TXT files) were imported into dChip (http://www.hsph.harvard.edu/cli/complab/dchip/; Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004;20:1233-40) and probe level values summarized. Data were exported and normalized using the reference normalization algorithm (Pounds S, Cheng C, Mullighan C, Raimondi SC, Shurtleff S, Downing JR. Reference alignment of SNP microarray signals for copy number analysis of tumors. Bioinformatics 2009;25:315-21). This algorithm uses user supplied or computationally detected diploid chromosomes to guide normalization of the entire array on a sample-by-sample basis, and optimizes normalization of complex cancer samples while eliminating batch effects. This procedure generates the .cnmz file that includes both the summarize, normalized prove intensities and the genotype data. "	"Optimally normalized data were subjected to paired circular binary segmentation (Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007;23:657-63) with thresholds set to detect copy number segments of &gt;2.3 or &lt;.7 copies and at least 5 markers (250K data) or 8 markers (SNP6 data). Raw copy number segmentation results inspected and curated in dChip."
Protocol Parameters						
Protocol Hardware						
Protocol Software						
Protocol Contact						
SDRF File	TARGET_ALL_CopyNumberArray_Phase1_20160812.sdrf.txt					
Term Source Name	NCBITaxon	NCIt	MO	EFO	OBI	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	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						