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Epigenomics Transfers Prostate Cancer Dx To GeneChip; Clinical Trials to Start in '07

Epigenomics said this week that it has transferred its prostate cancer molecular classification test to the Affymetrix GeneChip platform, and that it plans to begin testing the product in clinical trials next year with an eye on gaining US Food and Drug Administration 510(k) clearance in 2008.
The announcement comes six months after Epigenomics signed an agreement with Affy through its Powered by Affymetrix program to deploy diagnostic content on GeneChips for clinical use, a model pioneered by Roche and Affy’s AmpliChip drug-metabolism test. That diagnostic was cleared by the FDA two years ago (see BAN 7/5/2006, BAN 12/15/2004).
Epigenomics’ plans also reinforce the applicability of array-based DNA-methylation technology at a time when other array companies like NimbleGen, Illumina, and Agilent Technologies are showing interest in the area.
According to Achim Plum, vice president of corporate communications at Epigenomics, the test, based on the PITX2 biomarker, “would definitely be the first DNA methylation test for diagnostic use.”
“We are not aware of any in vitro kittable methylation diagnostic approved … out there,” he told BioArray News this week.
In a statement, Epigenomics said it has completed a concordance study that demonstrated that “the prototype real-time PCR assays used in the research phase” of developing the prostate cancer test could be transferred to the Affymetrix platform. Researchers observed a 97.8-percent agreement between the two platforms, the company said.

“Our depth of prior experience with DNA methylation microarrays made it possible to achieve this important step in product development in such a short timeline,” said Michael Wandell, head of product development at Epigenomics. “We are now looking forward to moving this product into clinical validation.”
The German diagnostics company will now turn its attention to testing the platform in clinical trials in 2007.
Epigenomics’ test uses PITX2 as a marker to help physicians predict outcomes for patients who have undergone radical prostatectomy. The company claims the test can separate post-prostatectomy cancer patients into two groups: those with a high likelihood of cancer recurrence and those with a low likelihood.  
The firm said it will review its clinical study plan with the FDA later this week in a pre-investigational device exemption meeting, and then immediately begin recruiting patients for the clinical trials, which will be conducted in the US and Europe.
“Based on an early collaboration meeting with the FDA in August this year, Epigenomics is confident that it will fulfill regulatory requirements through submission of a ‘de novo 510(k)’ for this test,” the company noted.
According to Plum, the company could begin marketing the test sometime in 2008.
“We’ll file an IDE some time in Q1, and clinical trials will be initiated some time mid next year, and basically the message is that we’ll bring out this test in 2008,” he told BioArray News this week.
He said Epigenomics will “send samples that [it has] collected from various sites to about four clinical trial sites that have the machines there placed by us, and they will run these assays under their conditions – with the prototype and the kits and so on.” He added that the company will probably select three sites in the US and one in Europe for the trials.

“We’ll file an IDE some time in Q1, and clinical trials will be initiated some time mid next year, and basically the message is that we’ll bring out this test in 2008.”

He added that the company was pleased with the transition from RT-PCR to arrays, noting that there were economic and product-related arguments for using an array over an RT-PCR assay in the clinical market, even if the test is based on a single marker, as Epigenomics’ is.
“If you think about the economics, if you have a real-time PCR assay that you want to use as a diagnostic, you need a real-time PCR license from Roche, and that is very expensive,” Plum said. He added that companies like Epigenomics could benefit from Affy’s existing installed base when launching their tests. “Roche has a test on it already, and other companies are coming out with tests, and so with each test that comes out, you make better use of the platform so the end user can run multiple assays on the same platform, and at the same time you have multiple sales forces, including the installed base,” he said.
He added that while the company only employs one marker in its prostate cancer test it made sense going forward to switch to an array format because future Epigenomics tests may use more markers.
“If you think about a product pipeline, where you have products that require more markers, you can [add more to] the very same platform,” he said. “The nice thing here is that the cost of goods doesn't scale with the number of markers linearly. So certainly they scale a bit because you also need PCR pre-amplification and so on, but not to the same extent as if you need real-time PCR probes,” Plum said.

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