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Epigenomics' Oncotype Dx Competitor May Run on Affy GeneChip Platform


Epigenomics said this week that Affymetrix had granted it non-exclusive rights to develop microarray-based in vitro diagnostics on its platform, including a potential rival to Genomic Health's Oncotype Dx.

The development meshes well with Epigenomics' previously announced plan to partner with a third party to carry out concordance studies to replace Roche's LightCycler as the platform for Epigenomics' tissue-based diagnostics. "We're going to go into a collaboration with a diagnostics platform device company" by the end of summer, Oliver Schacht, the company's CFO, told Pharmacogenomics Reporter in May. "It's probably going to be an array-based system."

An Epigenomics spokesperson could not be contacted before press time for this article.

The company is planning to file its tissue-based prostate cancer-profiling test for premarket approval from the US Food and Drug Administration before the end of 2007, and it is hoping to do the same with a breast cancer test soon afterward, Schacht said. "It could be that we end up with a de novo 510(k), but all that does is chop off 90 days from the approval process," he said.

Epigenomics needed to replace Roche Diagnostics after the diagnostics giant — a former partner in developing the tissue-based tests — backed out of the collaboaration. Roche would have been responsible for producing regulatory filings and performing clinical development, but it released the rights to both cancer-profiling tests to Epigenomics in February. "We're going to be running full clinical trials on the prostate and the breast products here over the next 18 to 24 months," said Schacht in February. "Our goal is to have FDA-approved in vitro diagnostic products on the market by 2008."

Epigenomics continues to work with Roche on three blood-based cancer detection tests: a prostate cancer test, a colorectal cancer test, and a breast cancer test. The company also plans to develop a blood-based lung cancer-screening test alone.

Although Epigenomics is profiling tissue based on DNA methylation markers, it is hoping to achieve results similar to Oncotype Dx, which profiles based on RNA expression patterns. "It's exactly the same medical question, and the question basically is, 'A woman following surgery is always going to get either tamoxifen or in the future aromatase inhibitors. Would [she] also require chemotherapy to prevent relapse, or could you do without the chemotherapy because the risk of relapse is really very small?'" Schacht said last month.

Approximately 200,000 women in the United States are diagnosed with early-stage estrogen-receptor positive, node-negative breast cancer every year, all of whom may benefit from a profiling test, said Schacht.

Epigenomics said this week that the recent agreement with Affy complements its strategic alliance with Qiagen for sample preparation, which was announced last year. For diagnostic purposes, Qiagen will market and sell products containing its bisulfite technology for use with Epigenomics' technologies and products. Under an OEM agreement, Qiagen will also provide Epigenomics with kit components for molecular diagnostic products.

In related news, Epigenomics and the Wellcome Trust Sanger Institute said this week that they had released epigenetic data for human chromosomes 6, 20, and 22 as part of the Human Epigenome Project, which was launched in 2003. The project has studied more than 2,500 loci, and has found about 21 percent of them to be differentially methylated.

Epigenomics said that detailed results of the study will be published "over the coming months." The company has patented the results, and said it will use the data for the development of diagnostic products.

The data from the study is available for non-commercial research use at and

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