MAGE-TAB Version	1.1
Investigation Title	TARGET: Ambiguous Lineage Acute Leukemia (ALAL) Phase III 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)	Hunger	Mullighan	Loh	Ma	Novik
Person First Name			Stephen	Charles	Mignon	Yussanne	Karen
Person Mid Initials			P			P	L
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	hungers@chop.edu	charles.mullighan@stjude.org	lohm@peds.ucsf.edu	yma@bcgsc.ca	knovik@bcgsc.ca
Person Phone	+1 301 451 8027	+1 888 478 4423		+1 901 595 3387	+1 415 476 3831	+1 604 707 5800 Ext 6082	+1 604 707 8000 Ext 7983
Person Fax	+1 301 480 4368			+1 901 595 5947		+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	3401 Civic Center Blvd Philadelphia, PA 19104	262 Danny Thomas Place, Mail Stop 342, Memphis TN 38105	Box 0106, UCSF	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	Children's Hospital of Philadelphia	St Jude Children's Research Hospital	UCSF Benioff Children's Hospital	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	investigator	investigator;data analyst;submitter	investigator
Person Roles Term Source REF	EFO;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 175 fully characterized patient cases with relapsed precursor B-cell ALL (all tumor/normal pairs, 85 with relapse sample as well) that will make up Phase II of the TARGET ALL dataset, each with gene expression, tumor and paired normal copy number analyses, and comprehensive next-generation sequencing to include whole genome sequencing, mRNA-seq and miRNA-seq. Subsets of these cases will also have methylation and/or whole exome sequencing data available as well. There are additionally a large number of cases with partial molecular characterization 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 genomics projects. Please see the TARGET Publication Guidelines at the OCG websitefor updated details on sharing of any TARGET substudy data."
Protocol Name	stjude.org:Protocol:DNA-Extraction-Qiagen-QIAamp:01	stjude.org:Protocol:WXS-LibraryPrep-Illumina:01	stjude.org:Protocol:WXS-ExomeCapture-Illumina:01	stjude.org:Protocol:WXS-Sequence-Illumina-HiSeq2500:01	stjude.org:Protocol:WXS-BaseCall-Illumina:01	stjude.org:Protocol:WXS-ReadAlign: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
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"Genomic DNA was prepared from using the Qiagen QIAamp DNA Mini Kit (Qiagen, Valencia, CA, USA). Please see https://ocg.cancer.gov/programs/target/target-methods for full extraction protocol details."					
Protocol Parameters						
Protocol Hardware				Illumina HiSeq 2500		
Protocol Software						
Protocol Contact
SDRF File	TARGET_ALL_WXS_Phase3_20181025.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]	SRP011999
Comment[BioProject]	PRJNA89529
Comment[dbGaP Study]	phs000464
