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Pilot Project To Map Three Cancers
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I Genome Sequencing Centers

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A component of The Cancer Genome Atlas Pilot Project will be high-throughput genomic sequencing. This activity will be conducted by Genome Sequencing Centers (GSCs) that have extensive experience in large-scale genomic DNA sequencing.

During the pilot project, the GSCs will implement high-throughput PCR-directed sequencing of a large number of targets (both genes and candidate regions) as part of the characterization of the selected tumors. In the longer term, it will be desirable to conduct whole genome sequence analysis of individual tumor samples. Therefore, TCGA will include a technology development component and the NHGRI Genome Technology Program will also be addressing this goal.

The sequencing centers participating in the TCGA Pilot Project will receive quality-controlled samples of the tumor specimens from the Human Cancer Biospecimen Core Resource. The targets for the TCGA genomic sequencing studies will 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 Human Genome Project, a considerable amount of technology development and implementation was accomplished in large-scale sequencing centers. Accordingly, the GSCs will also have the opportunity to 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.

The output will be deposited into the project database as well as other public databases, including the trace file repository at the National Center for Biotechnology Information of the National Library of Medicine, NIH.

In 2006, NHGRI awarded funding to three centers as part of its Large-Scale Sequencing Research Network. Each center has been designated a GSC and will devote a significant portion of its efforts to TCGA. They are:

  • Broad Institute Sequencing Platform, Broad Institute of MIT and Harvard, Cambridge, Mass.
  • Washington University Genome Sequencing Center, Washington University School of Medicine, St. Louis, Mo.
  • Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.
National Cancer InstituteNational Human Genome Research InstituteNational Institutes of HealthDepartment of Health and Human