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Center for Cancer Genome Characterization


The Cancer Genome Characterization Center (CGCC) at the Broad Institute of MIT and Harvard brings together a team of investigators with extensive expertise in cancer and genomics, as well as a track record of setting and attaining milestones. As part of The Cancer Genome Atlas (TCGA) pilot project, we propose to accomplish the following objectives: (1) Characterize structural alterations (amplification, deletion and LOH) and gene expression in a large collection of cancer samples. Specifically, we will use microarrays to perform high-density SNP genotyping and RNA expression profiling. We will analyze 1000, 1500 and 2000 samples in years 1, 2 and 3, respectively - with costs decreasing to allow an increasing number of samples on a roughly constant budget. (2) Improve the cost and performance of SNP genotyping and RNA expression profiling, by designing new, more efficient arrays. In particular, we will decrease total costs by a factor of at least 2-fold for the same information content. By the end of the project, it will be possible to characterize genome alteration and gene expression in a collection of 15,000 cancer samples (the target suggested in NCI's report on TCGA) at a total cost of <$6M/year over a three-year period. These technologies will thus be ready for full scale up within TCGA. (3) Cross-validate, integrate, and analyze CGCC data to determine regions of genome alteration for high-throughput sequencing. (4) Rapidly share data with the cancer research community.


Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.