The opening plenary session at the American Association for Cancer Research annual meeting focused on how the decreasing costs and increasing capabilities of gene sequencing technologies are revolutionizing the study of cancer genetics. (See BioWorld Today, April 17, 2007.)

Mircroarray technologies, a less expensive option, also are contributing to the cancer genetics revolution. To that end, microarray pioneer Affymetrix Inc. launched the Collaborations for Cancer Research Program, which will provide financial support and GeneChip products to cancer researchers at universities, research institutes and medical centers.

While Affymetrix traditionally has been lumped in with the research tool provider set, the initial studies outlined within the Collaborations for Cancer Research Program have a distinctly clinical feel. If the studies are able to generate detailed genetic profiles of certain tumor types, that information could be used to create molecular diagnostics arrays for testing tissue samples from patients at risk for or suspected of having that particular type of cancer.

Molecular diagnostics would represent a new market for Affymetrix and could help offset the slower growth the company recently has experienced. In 2006, Santa Clara, Calif.-based Affymetrix reported total product and product related revenue of $324 million, compared to $350 million in 2005.

The Collaborations for Cancer Research Program initially will involve alliances with 30 European cancer researchers, although Affymetrix plans to expand the program into North America and Japan later this year. The company said in a news release that it will "help researchers obtain tools and training" as well as "partially fund selected research projects that demonstrate clinical utility."

Affymetrix also plans to sponsor a European cancer meeting in the second half of the year at which program participants can present and discuss their research.

The researchers will use Affymetrix's GeneChip microarrays and associated products to study bladder, breast, colon, colorectal, lung, ovarian, pancreatic, prostate, testicular and thyroid cancers, as well as acute myelogenous leukemia and lymphoma. Microarray applications will include copy number analysis, chromatin immunoprecipitation (ChIP), gene expression and splicing pattern analysis. Tiling arrays, which cover the entire human genome, will be integral in many of the studies.

For example, the Spanish National Cancer Research Center, of Madrid, Spain, will seek to identify determinants of epigenetic deregulation in colon cancer; Queen Mary University in London will conduct a comprehensive genomic and molecular analysis of pancreatic cancer; and the German Cancer Research Center in Heidelberg will perform functional and transcriptome profiling of tumor progression genes in lung cancer cell lines.

In another potentially diagnostics-focused move, Affymetrix said on Tuesday that it has partnered with NuGEN Technologies Inc., of San Carlos, Calif., to co-market the NuGEN WT-Ovation FFPE System. The system enables researchers to conduct GeneChip studies with only 50 nanograms of total RNA, potentially allowing analysis of FFPE (formalin-fixed, paraffin-embedded) tissue samples derived from clinical studies, which previously may have been inaccessible by traditional RNA amplification methods.

Affymetrix spokespersons were not available for comment.

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