TARGET Molecular Characterization Platforms

Researchers working at a large-scale sequencing center.

Credit: The Broad Institute of MIT and Harvard

Below are the technologies that Therapeutically Applicable Research to Generate Effective Treatments (TARGET) used over the years. The technologies and protocols varied for each disease project type.

All nucleic acid samples used in TARGET projects were quality tested for consistency using PicoGreen quantification and short tandem repeat genotyping methods, regardless of where the nucleic acid was originally extracted.

ALL Phase 1

Protocols used for TARGET's study of Acute Lymphoblastic Leukemia Phase 1 (ALL P1)
Methodology	Platform name	Center
Clinical	COG Protocols (POG 9906)
DNA Prep	Qiagen QIAamp DNA Minikit	Nationwide Children’s Hospital
RNA Prep	Invitrogen TRIzol	University of New Mexico
Gene Expression	Affymetrix U133 Plus 2.0 Array	University of New Mexico
Copy Number	Affymetrix SNP 500K Array	St. Jude Children's Research Hospital
Copy Number	Affymetrix SNP Array 6.0	St. Jude Children's Research Hospital
WGS, WGS-lite	Illumina HiSeq 2000/250	British Columbia Cancer Agency
WGS	Complete Genomics, Inc.,	Complete Genomics Inc. (CGI)
mRNA-seq	Illumina Hiseq 2000	British Columbia Cancer Agency
Kinome Seq	Sanger	British Columbia Cancer Agency
Targeted Recapture Seq	Sanger	British Columbia Cancer Agency

ALL Phase 2 (Expansion)

Protocols used for TARGET's study of Acute Lymphoblastic Leukemia Phase 2 (ALL P2)
Methodology	Platform name	Center
Clinical	COG Protocols (AALL03B1, AALL0232, P9906, AALL0331, ALL0434)
DNA Prep	Qiagen QIAamp DNA Minikit	Nationwide Children’s Hospital
RNA Prep	Invitrogen TRIzol	University of New Mexico
Gene Expression	Affymetrix U133 Plus 2.0 Array	University of New Mexico
Copy Number	Affymetrix SNP 6.0 Array	St. Jude Children's Research Hospital
WGS	Complete Genomics, Inc.	Complete Genomics Inc. (CGI)
WXS	Illumina Hi-Seq 2000	Baylor College of Medicine
mRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency
microRNA-seq	Illumina Hiseq 2000	British Columbia Cancer Agency
Methylation	HELP Assay with Roche NimbleGen	Weill Cornell Medical College

ALL Phase 3 (ALAL)

Protocols used for TARGET's study of Acute Leukemia of Ambiguous Lineage (ALAL)
Methodology	Platform name	Center
Clinical
Copy Number	Illumina Infinium Omni2.5 Exome8 Kit	St. Jude Children's Research Hospital
Methylation	Illumina Infinium MethylationEPIC	St. Jude Children's Research Hospital
WGS	Illumina HiSeq2500	St. Jude Children's Research Hospital
WXS	Illumina HiSeq2500	St. Jude Children's Research Hospital
mRNA-seq	Illumina HiSeq2000	St. Jude Children's Research Hospital

AML

Protocols used for TARGET's study of Acute Myeloid Leukemia (AML)
Methodology	Platform name	Center
Clinical	COG Protocols (CCG-2961, AAML03P1, AAML0531)
DNA and RNA Prep	Qiagen AllPrep (DNA/RNA), mirVana (total and small RNAs)	Fred Hutchinson Cancer Research Center
Gene Expression	Affymetrix Gene ST Array	Hudson Alpha, Fred Hutchinson Cancer Research Center
Copy Number	Affymetrix SNP 6.0 Array	Fred Hutchinson Cancer Research Center
Methylation	Illumina Infinium 27K	Johns Hopkins University
Methylation	Illumina Infinium 450K	Phoenix Children's Hospital
WGS	Complete Genomics, Inc.	Complete Genomics Inc. (CGI)
WXS	Illumina Hi-Seq 2000	Baylor College of Medicine
mRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency
Targeted Capture Seq	Illumina Hi-Seq 2500	British Columbia Cancer Agency and Fred Hutchinson Cancer Research Center

AML Induction Failure

Protocols used for TARGET's study of Acute Myeloid Leukemia - Induction Failure (AML-IF)
Methodology	Platform name	Center
Clinical Annotation	COG Protocols (AAML0531, AAML03P1)
DNA and RNA Prep	Qiagen AllPrep (DNA/RNA) and mirVana (total and small RNAs)	Fred Hutchinson Cancer Research Center
mRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency
microRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency

Kidney - Wilms Tumor

Protocols used for TARGET's study of Wilms Tumor (WT)
Methodology	Platform name	Center
Clinical Annotation	NWTS – 5 Protocol
DNA and RNA Prep	Qiagen AllPrep kit (DNA/RNA) and mirVana (total and small RNAs)	Nationwide Children’s Hospital
Gene Expression	Affymetrix U133 Plus 2.0 Array	Lurie Children's Hospital Research Center
Copy Number	Affymetrix SNP 6.0 Array	St. Jude Children's Research Hospital, Lurie Children's Hospital Research Center
Methylation	Illumina Infinium 450K	Lurie Children's Hospital Research Center
WGS	Complete Genomics, Inc.	Complete Genomics, Inc.
WXS	Illumina Hi-Seq 2000	Baylor College of Medicine
mRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency
microRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency
Targeted Capture Seq	Illumina Hi-Seq 2500	British Columbia Cancer Agency and Fred Hutchinson Cancer Research Center

Kidney - Clear Cell Sarcoma

Protocols used for TARGET's study of Clear Cell Sarcoma of the Kidney (CCSK)
Methodology	Platform name	Center
Clinical	NWTS-5 Protocol
DNA and RNA Prep	Qiagen AllPrep kit (DNA/RNA) and mirVana (total and small RNAs)	Nationwide Children’s Hospital
Gene Expression	Affymetrix U133 Plus 2.0 Array	Lurie Children's Hospital Research Center
Copy Number	Affymetrix SNP 6.0 Array	St. Jude Children's Research Hospital, Lurie Children's Hospital Research Center
Methylation	Illumina Infinium 450K	Lurie Children's Hospital Research Center
WGS	Complete Genomics Inc. (CGI)	Complete Genomics Inc. (CGI)
mRNA-seq	Illumina Hi-Seq 2000	NCI Center for Cancer Research

Kidney - Rhabdoid Tumor

Protocols used for TARGET's study of Rhabdoid Tumor (RT)
Methodology	Platform name	Center
Clinical Annotation	AREN03B2 or NWTS-5 Protocols
DNA and RNA Prep	Qiagen AllPrep kit (DNA/RNA) and mirVana (total and small RNAs)	Nationwide Children’s Hospital
WGS	Illumina Hi-Seq 2000/2500	British Columbia Cancer Agency
mRNA-seq	Illumina Hiseq 2000	British Columbia Cancer Agency
microRNA-seq	Illumina Hiseq 2000	British Columbia Cancer Agency
Bisulfite-seq	Illumina Hi-Seq 2500
ChIP-seq	Illumina Hi-Seq 2000

Neuroblastoma

Protocols used for TARGET's study of Neuroblastoma (NBL)
Methodology	Platform name	Center
Clinical Annotation	COG NBL Protocols
DNA and RNA Prep	Qiagen AllPrep kit (DNA/RNA) and mirVana (total and small RNAs)	Nationwide Children’s Hospital (after 2013)
DNA Prep	Qiagen Genomic-Tips	Nationwide Children’s Hospital (prior 2013)
RNA Prep	Invitrogen TRIzol and Qiagen RNAeasy	Nationwide Children’s Hospital (prior 2013)
Gene Expression	Affymetrix Human Exon ST Array	Children's Hospital Los Angeles, Children's Hospital of Philadelphia, or Children's Oncology Group Biopathology Center at Colombus, Ohio.
Copy Number	Illumina HumanHap 550K Beadchip	Children's Hospital of Philadelphia
Methylation	Illumina Infinium 450K	USC Epigenome Center
WGS	Illumina Genome Analyzer IIx or Hi-Seq 2000	British Columbia Cancer Agency
WGS	Complete Genomics Inc.	Complete Genomics Inc.,
WXS	Illumina Genome Analyzer II or Hi-Seq 2000	Broad Institute
WXS (MDLS models)	Illumina Hi-Seq 2000	Baylor College of Medicine
mRNA-seq	Illumina Hi-Seq 2000	British Columbia Cancer Agency
mRNA-seq	Illumina Hi-Seq 2000	NCI Center for Cancer Research
Targeted Capture Seq	Illumina Hi-Seq 2500	British Columbia Cancer Agency and Fred Hutchinson Cancer Research Center

Osteosarcoma

Protocols used for TARGET's study of Osteosarcoma (OS)
Methodology	Platform name	Center
Clinical Annotation	COG & SickKids Protocols
DNA and RNA Prep	Qiagen AllPrep kit (DNA/RNA) and mirVana (total and small RNAs)	Nationwide Children’s Hospital
Gene Expression	Affymetrix Human Exon ST Array	Children’s Hospital of Los Angeles, Texas Children’s Hospital
Copy Number	Affymetrix SNP 6.0 Array	Children’s Hospital of Los Angeles
Methylation	Illumina Infinium 450K	Phoenix Children’s Hospital, Baylor College of Medicine
microRNA Profiling	MegaPlex TaqMan Array	Baylor College of Medicine
WGS	Complete Genomics Inc. (CGI)	Complete Genomics Inc. (CGI)

Model Systems

Protocols used for TARGET's Model Systems (MDLS) and Pediatric Preclinical Testing Program (PPTP)
Methodology	Platform name	Center
DNA Prep	Qiagen QIAamp DNA Minikit (ALL MDLS)	Nationwide Children’s Hospital
RNA Prep	Invitrogen TRIzol (ALL MDLS)	University of New Mexico
Gene Expression	Affymetrix U133 Plus 2.0 Array (ALL MDLS; PPTP)	University of New Mexico (ALL MDLS)
Gene Expression	SurePrint G3 Human Gene Expression Array (PPTP)
Copy Number	Affymetrix SNP 6.0 Array (PPTP)	Nationwide Children's Hospital
Copy Number	Illumina Omni5 BeadChip (PPTP)	Nationwide Children's Hospital
WXS	Illumina Hi-Seq 2000 (NBL MDLS, PPTP)	Baylor College of Medicine