| Genome Sequencing Centers
TCGA’s Genome Sequencing Centers (GSCs) perform large-scale genomic sequencing using the most current technologies. During the Human Genome Project, a considerable amount of technology development and implementation was accomplished in large-scale sequencing centers making programs like TCGA feasible. Accordingly, the GSCs have the opportunity to continually improve existing technology and invest in implementation of new sequencing technologies with the long-term goal of enabling whole genome sequencing of tumors for complete genomic analysis at an increasingly reduced cost. All sequencing data are available in the TCGA Data Portal or from the TCGA page at NIH’s database of Genotype and Phenotype (dbGaP).
Throughout the pilot project, the GSCs have continued to evolve their approaches, as seen in this brief timeline:
| October 2008: |
TCGA publication includes polymerase chain reaction/Sanger dideoxy method sequencing of  601 target genes. |
| March 2009: |
GSCs introduce hybrid-capture procedure and second generation sequencing instruments for analysis of more than 6000 known cancer-associated target genes and miRNAs. |
| July 2009: |
GSCs submit first of 24 whole genome sequence analyses of glioblastoma multiforme and Ovarian tumor samples. |
Target Gene/miRNA Selection
The targets for the TCGA genomic sequencing studies consist of genes and candidate regions selected by two different approaches. In one approach genes of interest (e.g., tumor repressors or oncogenes) are identified from the scientific literature and by consultation with experts in the field. In the second approach, genes and genomic regions are identified by analyses of the data produced by the TCGA Cancer Genome Characterization Centers (CGCCs). During the expansion phase of TCGA, the Research Network expects to be able to shift to an entirely unbiased whole exome sequencing approach instead of the 6,000+ gene approach.
View more than 6,000 target genes and microRNAs (miRNAs) being sequencing by the GSC.
NHGRI awarded funding to three centers as part of its Large-Scale Sequencing Research Network. These three GSCs are:
- Broad Institute Sequencing Platform, Broad Institute, Cambridge, Mass.
Principal Investigator: Eric Lander, Ph.D.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
Principal Investigator: Richard Gibbs, Ph.D.
- Washington University Genome Sequencing Center, Washington University School of Medicine, St. Louis, Mo.
Principal Investigator: Richard Wilson, Ph.D.
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