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| Cancer Genome Characterization Centers
In 2006, the NCI awarded a total of $11.7 million per year to support the Cancer Genome Characterization Centers (CGCCs). The CGCCs support The Cancer Genome Atlas (TCGA) in accelerating the understanding of the molecular basis of cancer. Each center uses advanced and complementary analysis technologies to strategically characterize genomic and epigenomic changes in cancer. The CGCCs are providing a catalog of the deletions, rearrangements, amplifications of large chromosomal segments, transcriptional alterations, changes in methylation and are identifying areas of the genome (i.e. specific genes) for mutation analysis by the Genome Sequencing Centers. All data produced by the CGCCs are publicly available through the TCGA Data Portal, with respect to patient privacy and confidentiality.
The TCGA Cancer Genome Characterization Centers for the pilot project are listed below along with the type of analysis and platform(s) currently in use (as of September 2009).
| CGCC Name and Location |
Principal Investigators |
Type of Analysis Performed |
Examples of Platforms Utilized |
| Broad Institute of MIT and Harvard, Cambridge, Mass. |
Matthew Meyerson, M.D., Ph.D. |
Gene Expression Profiles |
GeneChip® HT Human Genome U133 Array Plate Set |
| Copy Number Alterations |
Affymetrix Genome-Wide Human SNP Array 6.0 |
| Harvard Medical School and Brigham and Women’s Hospital, Boston, Mass. |
Raju Kucherlapati, Ph.D.
Lynda Chin, M.D. |
Gene Expression Profiles |
Illumina Genome Analyzer mRNA Digital Gene Expression |
| Copy Number Alterations |
Agilent Human Genome CGH Custom Microarray 2x415K |
| Lawrence Berkeley National Laboratory, Berkeley, Calif. |
Joe Gray, Ph.D.
Paul Spellman, Ph.D. |
Gene Expression Profiles |
Affymetrix Human Exon 1.0 ST Array |
| Memorial Sloan-Kettering Cancer Center, New York, N.Y. |
Marc Ladanyi, M.D. |
Copy Number Alterations |
Agilent SurePrint G3 Human CGH Microarray Kit 1x1M |
| The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Md., and University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, Calif. |
Peter Laird, Ph.D.
Stephen Baylin, M.D. |
Methylation Profiles |
Illumina Infinium Human DNA Methylation 27 |
| HudsonAlpha Institute for Biotechnology, Huntsville, Ala. |
Rick Wilson, Ph.D. |
Copy Number Alterations |
Illumina Human1M-Duo BeadChip |
| University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, N.C. |
Chuck Perou, Ph.D. |
Gene Expression Profiles |
Agilent 244K Custom Gene Expression G4502A-07-3 |
| miRNA Expression Profiles |
Agilent Human miRNA Microarray Rel12.0 |
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