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Going 'Broad' to get specific about cancer
SANTA CLARA, Calif.—Affymetrix Inc. will be bringing its Genome-Wide Human SNP 6.0 Array to bear in a collaborative agreement it has entered into with the Broad Institute of MIT and Harvard to chart the genomic changes involved in more than 20 kinds of cancer as part of the Broad's work in The Cancer Genome Atlas (TCGA).
Specifically, the agreement calls for the processing of 13,500 cancer samples on the Affymetrix Genome-Wide Human SNP 6.0 Array, which is a widely used platform for genotyping and studying copy number variation (CNV) and somatic events in tumor samples.
Affymetrix reports that the SNP Array 6.0 will also help determine loss of heterozygosis, a genomic change that Affymetrix notes is important because it indicates a loss of normal function and it is something that cannot be detected using traditional cytogenetic methods such as fluorescent in-situ hybridization (FISH) or comparative genomic hybridization (CGH).
High resolution and a hybrid SNP- CNV array design are what make the SNP Array 6.0 the right choice for the Broad and TCGA in studying the complexities of cancer genomes, according to 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," he says.
Although the relationship with Affymetrix is important, this isn't the Broad's first partner in major TCGA work. For example, the institute teamed up recently with the Dana-Farber Cancer Institute in an effort called Project Achilles that is aimed at developing a systematic way of pinpointing various cancers' weak spots. When researchers involved in TCGA recently reported that 1,800 genes in the ovarian cancer genome are repeatedly amplified, the Project Achilles team harnessed the TCGA data to rapidly determine which of the genes are essential to ovarian tumor growth, says William Hahn, a senior associate member of the Broad and an associate professor at Dana-Farber, who noted at the time, "Not only can we characterize what genes are mutated or altered, but we can also simultaneously assess which of those are important functionally."
TCGA got its start in 2006 thanks to an investment of $50 million each from the National Cancer Institute and National Human Genome Research Institute, and it was created as a three-year pilot. After early promising successes, the National Institutes of Health announced in September 2009 an investment of $275 million over the following two years to extend the program.
By using technology like that of Affymetrix's, researchers 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," according to 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."
Nearly two weeks after announcing the collaboration with the Broad Institute, Affymetrix inked another important 'omics- and array-related deal, entering into an exclusive, worldwide licensing agreement with Genisphere LLC for RNA amplification and labeling technology to address challenging sample types, including formalin-fixed, paraffin-embedded (FFPE) samples. FFPE samples are often sought for cancer and translational research but remain a largely untapped source of valuable data for discovering biomarkers and clinically relevant gene expression profiles to advance the understanding of diseases.
"This agreement advances the Affymetrix vision of growing our microarray business within targeted applications where array-based approaches provide more cost-effective solutions, highly accurate data and the most relevant gene-expression content compared to competing technologies," said Dr. Kevin Cannon, general manager of the Gene Expression Business Unit at Affymetrix, of the Genisphere deal.
"In today's competitive market, it is critical to provide researchers with the right tool for the specific application. The strategic addition of Genisphere's RNA amplification and labeling solution for FFPE samples is a perfect complement to the Affymetrix microarray portfolio, providing researchers a complete workflow solution from whole-genome analysis of clinically challenging FFPE samples to validation of single genes."