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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).

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