SANTA CLARA, Calif.–Affymetrix, Inc. (NASDAQ:AFFX) today announced that the company has entered into an agreement with the Broad Institute to chart the genomic changes involved in more than 20 types of cancer as part of the Broad’s work in The Cancer Genome Atlas (TCGA). The agreement will involve the processing of 13,500 cancer samples on the Affymetrix® Genome-Wide Human SNP 6.0 Array, a widely used platform for genotyping and studying copy number variation (CNV) and somatic events in tumor samples. The SNP Array 6.0 will also determine loss of heterozygosity (LOH), an important genomic change that indicates a loss of normal function that cannot be detected using traditional cytogenetic methods such as FISH or comparative genomic hybridization (CGH).

“High resolution and a hybrid SNP-CNV array design make the SNP Array 6.0 ideal for studying the complex cancer genome,” said Andy Last, Chief Commercial Officer at Affymetrix. “Mapping this disease using SNP 6.0’s range of analysis tools—from upfront sample control to downstream sequencing validation—will profoundly improve our understanding of genetic drivers associated with these cancers.”

With an investment of $50 million each from the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), TCGA began in 2006 as a three-year pilot. Following its initial success, the National Institutes of Health (NIH) announced in September 2009 an investment of $275 million over the next two years of this five-year program. To date, TCGA has achieved comprehensive sequencing, characterization, and analysis of the genomic changes in samples from brain, ovarian, and prostate cancers.

“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,” said Matthew Meyerson, a senior associate member at the Broad Institute, a TCGA principal investigator, and director of the Center for Cancer Genome Discovery at Dana-Farber Cancer Institute. “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.”

There are at least 200 forms of cancer and many more subtypes. Each of these is caused by errors in DNA that cause cells to grow uncontrolled. TCGA aims to identify the changes in each cancer’s complete set of DNA?its genome?and to understand how such changes interact to drive the disease. The ultimate goal of the project is to lay the foundation for improving cancer prevention, early detection, and treatment.

To date, TCGA has confirmed that an atlas of changes could be created for specific cancer types. It has also shown that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale, and develop an infrastructure for making the data publicly accessible. Importantly, it has proven that making the data freely available would enable researchers anywhere around the world to make and validate important discoveries.

About Affymetrix

Affymetrix technology is used by the world’s top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government and nonprofit research institutes. More than 2,100 systems have been shipped around the world and more than 23,500 peer-reviewed papers have been published using the technology. Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Santa Clara, Cleveland, Ohio, and Singapore. The company has about 900 employees worldwide and maintains sales and distribution operations across Europe, Asia, and Latin America. For more information about Affymetrix, please visit http://www.affymetrix.com.