TCGA Molecular Characterization Platforms

Researchers working at a large-scale sequencing center.

Credit: The Broad Institute of MIT and Harvard

Technology changed dramatically during the 12 year span of the The Cancer Genome Atlas (TCGA) project. Shotgun sequencing of bacterial artificial chromosomes was the platform of choice for The Human Genome Project, which established the reference human genome and a foundation for TCGA. But at TCGA’s start in 2006, microarray-based technologies were leading the molecular characterization field.

Over the next decade, in part due to TCGA’s demand for scalable, low-cost data, high-throughput sequencing rapidly developed and became widely accessible to researchers.

Below are the technologies TCGA utilized and evaluated over the years. At the program’s close, TCGA employed microarrays for profiling copy number variants, methylation, and protein expression and high-throughput sequencing for characterizing DNA and RNA.

TCGA Characterization Platform Specifications
Center	TCGA Platform Code	DCC Platform Name	Instrument Support Materials	Sequence Download	TCGA ADF Download
Broad Institute of MIT and Harvard	ABI	Applied Biosystems Sequence data	3730/3730xl DNA Analyzers	Primers	N/A
McDonnell Genome Institute at Washington University	ABI	Applied Biosystems Sequence data	3730/3730xl DNA Analyzers	Primers	N/A
Human Genome Sequencing Center at Baylor College of Medicine	ABI	Applied Biosystems Sequence data	3730/3730xl DNA Analyzers	Primers	N/A
University of North Carolina	AgilentG4502A_07_1	Agilent 244K Custom Gene Expression G4502A-07-1	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
University of North Carolina	AgilentG4502A_07_2	Agilent 244K Custom Gene Expression G4502A-07-2	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
University of North Carolina	AgilentG4502A_07_3	Agilent 244K Custom Gene Expression G4502A-07-3	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
Memorial Sloan Kettering Cancer Center	CGH-1x1M_G4447A	Agilent SurePrint G3 Human CGH Microarray Kit 1x1M	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
Broad Institute of MIT and Harvard	Genome_Wide_SNP_6	Affymetrix Genome-Wide Human SNP Array 6.0	Genome-Wide Human SNP Array 6.0	FASTA	TCGA ADF
McDonnell Genome Institute at Washington University	Genome_Wide_SNP_6	Affymetrix Genome-Wide Human SNP Array 6.0	Genome-Wide Human SNP Array 6.0	FASTA	TCGA ADF
University of North Carolina	H-miRNA_8x15K	Agilent 8 x 15K Human miRNA-specific microarray	Human mouse and rat miRNA Microarray	FASTA	TCGA ADF
University of North Carolina	H-miRNA_8x15Kv2	Agilent Human miRNA Microarray Rel12.0	Human mouse and rat miRNA Microarray	FASTA	TCGA ADF
Memorial Sloan Kettering Cancer Center	HG-CGH-244A	Agilent Human Genome CGH Microarray 244A	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
Harvard Medical School	HG-CGH-244A	Agilent Human Genome CGH Microarray 244A	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
Harvard Medical School	HG-CGH-415K_G4124A	Agilent Human Genome CGH Custom Microarray 2x415K	SurePrint G3 CGH+SNP Microarray	FASTA	TCGA ADF
McDonnell Genome Institute at Washington University	HG-U133_Plus_2	Affymetrix Human Genome U133 Plus 2.0 Array	Human Genome U133 Array	FASTA	TCGA ADF
Broad Institute of MIT and Harvard	HT_HG-U133A	Affymetrix HT Human Genome U133 Array Plate Set	Human Genome U133 Array	TSV	TCGA ADF
Berkeley Lab	HuEx-1_0-st-v2	Affymetrix Human Exon 1.0 ST Array	Exon 1.0 ST Array	FASTA	TCGA ADF
HudsonAlpha Institute for Biotechnology	Human1MDuo	Illumina Human1M-Duo BeadChip	Infinium HD BeadChip DNA	FASTA	TCGA ADF
HudsonAlpha Institute for Biotechnology	HumanHap550	Illumina 550K Infinium HumanHap550 SNP Chip	Infinium BeadChip DNA	FASTA	TCGA ADF
Johns Hopkins - USC Epigenome Center	HumanMethylation27	Illumina Infinium Human DNA Methylation 27	Infinium Human DNA Methylation 27	See ADF File	TCGA ADF
Johns Hopkins - USC Epigenome Center	HumanMethylation450	Illumina Infinium Human DNA Methylation 450	Infinium Human DNA Methylation 450	See ADF File	TCGA ADF
Johns Hopkins - USC Epigenome Center	IlluminaDNAMethylation_OMA002_CPI	Illumina DNA Methylation OMA002 Cancer Panel I	GoldenGate DNA Methylation	FASTA	TCGA ADF
Johns Hopkins - USC Epigenome Center	IlluminaDNAMethylation_OMA003_CPI	Illumina DNA Methylation OMA003 Cancer Panel I	GoldenGate DNA Methylation	See ADF File	TCGA ADF
McDonnell Genome Institute at Washington University	IlluminaGA_DNASeq	Illumina Genome Analyzer DNA Sequencing	Genome Analyzer IIx	N/A	N/A
Broad Institute of MIT and Harvard	IlluminaGA_DNASeq	Illumina Genome Analyzer DNA Sequencing	Genome Analyzer IIx	N/A	N/A
Human Genome Sequencing Center at Baylor College of Medicine	IlluminaGA_DNASeq	Illumina Genome Analyzer DNA Sequencing	Genome Analyzer IIx	N/A	N/A
University of California Santa Cruz	IlluminaGA_DNASeq	Illumina Genome Analyzer DNA Sequencing	Genome Analyzer IIx	N/A	N/A
University of North Carolina	IlluminaGA_DNASeq	Illumina Genome Analyzer DNA Sequencing	Genome Analyzer IIx	N/A	N/A
BC Cancer Agency	IlluminaGA_miRNASeq	Illumina Genome Analyzer miRNA Sequencing	Genome Analyzer IIx	N/A	N/A
Harvard Medical School	IlluminaGA_mRNA_DGE	Illumina Genome Analyzer mRNA Digital Gene Expression	Genome Analyzer IIx	N/A	N/A
BC Cancer Agency	IlluminaGA_RNASeq	Illumina Genome Analyzer RNA Sequencing	Genome Analyzer IIx	N/A	N/A
University of North Carolina	IlluminaGA_RNASeqV2	Illumina Genome Analyzer RNA Sequencing Version 2 analysis	Genome Analyzer IIx	N/A	N/A
Harvard Medical School	IlluminaHiSeq_DNASeqC	Illumina HiSeq for Copy Number Variation	HiSeq 2000	N/A	N/A
BC Cancer Agency	IlluminaHiSeq_miRNASeq	Illumina HiSeq 2000 miRNA Sequencing	HiSeq 2000	N/A	N/A
University of North Carolina	IlluminaHiSeq_RNASeq	Illumina HiSeq 2000 RNA Sequencing	HiSeq 2000	N/A	N/A
University of North Carolina	IlluminaHiSeq_RNASeqV2	Illumina HiSeq 2000 RNA Sequencing Version 2 analysis	HiSeq 2000	N/A	N/A
University of North Carolina	IlluminaHiSeq_TotalRNASeqV2	Illumina HiSeq 2000 Total RNA Sequencing Version 2 analysis	HiSeq 2000	N/A	N/A
Johns Hopkins - USC Epigenome Center	IlluminaHiSeq_WGBS	Illumina HiSeq 2000 Bisulfite-converted DNA Sequencing	HiSeq 2000	N/A	N/A
MD Anderson Cancer Center	MDA_RPPA_Core	M.D. Anderson Reverse Phase Protein Array Core	MD Anderson RPPA Core Facility	N/A	N/A
Nationwide Children's Hospital	microsat_i	Microsatellite Instability Analysis	SOLiD 3 Plus	N/A	N/A
University of California Santa Cruz	SOLiD_DNASeq	ABI SOLiD DNA System Sequencing	SOLiD 3 Plus	N/A	N/A
Broad Institute of MIT and Harvard	SOLiD_DNASeq	ABI SOLiD DNA System Sequencing	SOLiD 3 Plus	N/A	N/A
Human Genome Sequencing Center at Baylor College of Medicine	SOLiD_DNASeq	ABI SOLiD DNA System Sequencing	SOLiD 3 Plus	N/A	N/A

Center: Name of the center that submitted data for the platform.

TCGA Platform Code: Code used by TCGA to represent the platform. The platform code is used in archive and file names as well as file contents.

DCC Platform Name: Name used by TCGA's Data Coordinating Center to represent the platform.

Instrument Support Materials: Data sheets or documentation of a platform provided by the vendor.

Sequence Download: Probe sequences of the platform. For array-based platforms, a download of the file (in FASTA or TSV format) that was submitted by the center and used to create the ADF file is provided. For sequence-based platforms, a link to the National Center for Biotechnology Information (NCBI) Trace or Short Read Archives. "N/A" indicates that sequence files are not applicable to the platform and that those sequences may be available in a result file (e.g. IlluminaGA_mRNA_DGE sequences are available in the archive result files).

TCGA ADF Download: Descriptions of the design of an array, i.e., positions of each sequence on an array and any associated annotations. TCGA used a modified format of the standard microarray gene expression tabular (MAGE-TAB) file. "N/A" indicate that ADF files are not applicable to the platform (e.g. IlluminaGA_mRNA_DGE is not an array-based platform and has no ADF).