MAGE-TAB Version	1.1
Investigation Title	TARGET: Neuroblastoma (NBL) 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)	Maris	Ma	Zhang
Person First Name			John	Xiaotu	Jinghui
Person Mid Initials			M		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	maris@chop.edu	xiaotu.ma@stjude.org	jinghui.zhang@stjude.org
Person Phone	+1 301 451 8027	+1 888 478 4423	+1 215 590 5244	+1 901 595 3774	+1 901 595 6829
Person Fax	+1 301 480 4368		+1 267 426 0685	+1 901 595 7100	+1 901 595 7100
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	3501 Civic Center Blvd CTRB 3060, Philadelphia, PA 19104	262 Danny Thomas Place, Memphis, TN 38105	262 Danny Thomas Place, Memphis, TN 38105
Person Affiliation	National Cancer Institute	National Cancer Institute	Children's Hospital of Philadelphia	St Jude Children's Research Hospital	St Jude Children's Research Hospital
Person Roles	funder;investigator	data coder;curator	investigator	investigator;data analyst;submitter	investigator;data analyst
Person Roles Term Source REF	EFO;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	"There are ~214 fully characterized patient cases with neuroblastoma (all tumor/normal pairs, 10 with relapse sample as well) that will make up the TARGET NBL dataset, along with some cell lines and xenografts. The dataset includes 24 4S cases as well. Each fully characterized case has gene expression, tumor and paired normal copy number analyses, methylation and comprehensive next-generation sequencing to include whole genome and/or whole exome sequencing. A majority of these cases will also have mRNA-seq and methylation data available as well. There are additionally a large number of cases, both low and high risk, with partial molecular characterization to include some next generation and targeted Sanger sequencing making this a large and informative genomic dataset. 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... (for more see dbGaP study page.)"
Protocol Name	nationwidechildrens.org:Protocol:DNA-Extraction-Qiagen-GenomicTips:01	broadinstitute.org:Protocol:WXS-LibraryPrep-Illumina:01	broadinstitute.org:Protocol:WXS-ExomeCapture-Agilent-WholeExome1.1RefSeqPlus3Boosters:01	broadinstitute.org:Protocol:WXS-Sequence-Illumina-GAII:01	broadinstitute.org:Protocol:WXS-Sequence-Illumina-HiSeq2000:01	broadinstitute.org:Protocol:WXS-BaseCall-Illumina:01	broadinstitute.org:Protocol:WXS-ReadAlign:01	broadinstitute.org:Protocol:WXS-CnvSegment:01	stjude.org:Protocol:WXS-VariantCall-Bambino-DToxoG:01
Protocol Type	nucleic acid extraction protocol	nucleic acid library construction 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
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"Please see https://ocg.cancer.gov/programs/target/target-methods for full extraction protocol details."								"Of the 1,131 paired tumor-normal WES data, all except for 23 osterosarcoma pairs exhibit the expected binomial distribution of variant allele fraction for known germline SNPs. The 23 outlier samples were not used for discovery of driver genes due to their abnormal profile of variant allele distribution. They were included only for determining mutation prevalence of the driver genes identified in this study. Somatic SNVs and indels were detected by the Bambino program followed by postprocessing and manual curation as previously described. As 8-oxo-G artifact has been reported previously, we implemented an 8-oxo-G filter following the principles described in the D-ToxoG (http://archive.broadinstitute.org/cancer/cga/dtoxog) algorithm. The filter was tested on the "Exome_Native" neuroblastoma samples known to have 8-oxo-G artifacts and then applied to the variants identified in all WES data set."
Protocol Parameters						Software Versions			
Protocol Hardware				Illumina Genome Analyzer II	Illumina HiSeq 2000				
Protocol Software						GAPipeline			
Protocol Contact
SDRF File	TARGET_NBL_WXS_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]	SRP012002
Comment[BioProject]	PRJNA89523
Comment[dbGaP Study]	phs000467
