TCGA Molecular Characterization Platforms
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.
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).