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Affymetrix, Broad Institute Collaborate for The Cancer Genome Atlas

NEW YORK (GenomeWeb News) – Affymetrix today announced a collaboration with the Broad Institute to chart the genomic changes in more than 20 cancer types as part of the Broad's work on The Cancer Genome Atlas.

About 13,500 cancer samples will be processed on the Affymetrix Genome-wide Human SNP 6.0 Array as part of the partnership. Copy number variation and somatic events will also be studied using the array, as will determining the loss of heterozygosity.

Financial terms of the deal were not disclosed.

“By using this technology, we are able to map many types of changes in the cancer genome, including gains and losses of genetic material, at high resolution and in a cost-effective manner,“ Matthew Meyerson, a senior associate member at Broad, a TCGA principal investigator, and director of the Center for Cancer Genome Discovery at Dana-Farber Cancer Institute, said in a statement. “Furthermore, we are able to evaluate cancer specimen features, such as sample integrity and tumor cell purity, which are highly useful adjuncts for next-generation DNA sequencing,“ he added.

TCGA was started in 2006 as a three-year pilot study with a $50 million investment each from the National Cancer Institute and the National Human Genome Research Institute. In September 2009, the NIH announced an investment of $275 million over the next two years of the five-year program. The program has achieved a “comprehensive sequencing, characterization, and analysis“ of genomic changes in brain, ovarian, and prostate cancer, so far, Affy said.

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