MAGE-TAB Version	1.1
Investigation Title	TARGET: Acute Myeloid Leukemia (AML) Targeted-Capture
Experimental Design
Experimental Design Term Source REF
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)	Meshinchi	Arceci	Ma	Novik
Person First Name			Soheil	Robert	Yussanne	Karen
Person Mid Initials				J	P	L
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	smeshinc@fredhutch.org	rarceci@phoenixchildrens.com	yma@bcgsc.ca	knovik@bcgsc.ca
Person Phone	+1 301 451 8027	+1 888 478 4423	+1 206 667 4077	+1 602 827 2508	+1 604 707 5800 Ext 6082	+1 604 707 8000 Ext 7983
Person Fax	+1 301 480 4368		+1 206 667 4310	+1 602 271 0264	+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	1100 Fairview Avenue North, D5-380, POB 19024, Seattle, WA  98109	445 N. 5th St, Tgen Building Room 322, Phoenix, AZ 85004	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	Fred Hutchinson Cancer Research Center	Phoenix 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;data analyst;submitter	investigator
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 200 fully characterized patient cases with AML (all tumor/normal pairs, 100 with relapse sample as well) that will make up the TARGET AML dataset, each with gene expression, tumor and paired normal copy number analyses, methylation and comprehensive next-generation sequencing to include whole genome sequencing, mRNA-seq and miRNA-seq. A subset of these cases will also have 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	fredhutch.org:Protocol:DNA-Extraction-Qiagen-AllPrep:01	bcgsc.ca:Protocol:TargetedCapture-LibraryPrep-Illumina:01	bcgsc.ca:Protocol:TargetedCapture-Sequence-Illumina-HiSeq2000:01	bcgsc.ca:Protocol:TargetedCapture-Sequence-Illumina-HiSeq2500:01	bcgsc.ca:Protocol:TargetedCapture-BaseCall-Illumina:01	bcgsc.ca:Protocol:TargetedCapture-ReadAlign:01	bcgsc.ca:Protocol:TargetedCapture-Mpileup-Vcf2Maf:01	bcgsc.ca:Protocol:TargetedCapture-VariantCall-Mpileup:01	bcgsc.ca:Protocol:TargetedCapture-VariantCall-Strelka:01
Protocol Type	nucleic acid extraction 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	data transformation protocol
Protocol Term Source REF	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."	"Probe design for custom capture validation sequencing: Probes were designed using Agilent's SureDesign online web-based tool, located at URL: https://earray.chem.agilent.com/suredesign/. There were 420 targets provided as HUGO gene symbols along with 560 RefSeq IDs. RefSeq IDs were used in order to avoid ambiguity in targeting the incorrect isoform of a gene symbol. In addition to these 560 RefSeqIDs, 15 genomic positions were also included in the target region. During the design phase, the RefSeq IDs were limited to coding exons, UTRs (both 5' and 3' UTR). Each region was padded with an additional 10 bases on both the 5' and 3' ends. This resulted in an overall target space of 2.376 Mbp (megabase pairs). Probe density was specified at 2x, with moderately stringent repeat masking, and balanced boosting options selected. According to the Agilent SureDesign report, 43,137 probes were designed for a total size 2.785 Mbp (this total counts overlapping bases in adjacent probes separately). 98.7144% of the 2.376 Mbp target region was covered by a probe. Custom Java code was developed at the British Columbia Cancer Agency Genome Sciences Centre (BCGSC) to independently verify the accuracy of the probe design. This code incorporated a BLAT alignment of each probe against the reference genome (H. sapiens, hg19, GRCh37, February 2009) to ensure the target region was covered. Once the probe design was verified, Agilent SureSelect XT Custom 0.5-2.9Mb probes were ordered. Whole genome library construction and multiplex custom gene capture: Genomic DNA libraries from which gene regions of interest are captured were constructed according to British Columbia Cancer Agency Genome Sciences Centre (BCGSC) plate-based and paired-end library protocols on a Biomek FX liquid handling robot (Beckman-Coulter, USA). Briefly, 1ug of high molecular weight genomic DNA was sonicated (Covaris E210) in a 60uL volume to 200-300bp. Sonicated DNA was purified with magnetic beads (Agencourt, Ampure). The DNA fragments were end-repaired, phosphorylated and bead purified in preparation for A-tailing. Illumina sequencing adapters were ligated overnight at 20oC and adapter ligated products bead purified and enriched with 4 cycles of PCR using primers containing a hexamer index that enables library pooling. 94ng from each of 19 to 24 different libraries were pooled prior to custom capture using Agilent SureSelect XT Custom 0.5-2.9Mb probes. The pooled libraries were hybridized to the RNA probes at 65oC for 24 hours. Following hybridization, streptavidin-coated magnetic beads (Dynal, MyOne) were used for custom capture. Post-capture material was purified on MinElute columns (Qiagen) followed by post-capture enrichment with 10 cycles of PCR using primers that maintain the library-specific indices."	"Paired-end 100 base reads were sequenced per pool in a single lane of an Illumina HiSeq2000 instrument."	"Paired-end 100 base reads were sequenced per pool in a single lane of an Illumina HiSeq2500 instrument."					
Protocol Parameters					Software Versions				
Protocol Hardware			Illumina HiSeq 2000	Illumina HiSeq 2500					
Protocol Software					Illumina RTA				
Protocol Contact
SDRF File	TARGET_AML_Targeted-Capture_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]	SRP012000
Comment[BioProject]	PRJNA89525
Comment[dbGaP Study]	phs000465
