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Epigenomics Takes Its First Solo Step In Development of Oncotype Dx Rival


This week, Epigenomics said it had validated two prognostic markers for a breast-cancer diagnostic that could compete with Genomic Health's Oncotype Dx, but was abandoned by former partner Roche Diagnostics, the company said this week.

The study examined the use of Epigenomics' main DNA methylation biomarker, PITX2, as well as a secondary marker, to predict breast cancer recurrence in 395 patients with estrogen receptor-positive, node-positive cancer who had been treated with the chemotherapeutic anthracycline as adjuvant therapy.

According to Berlin-based Epigenomics, the test was able to identify 62 percent of patients who would experience metastasis-free survival for 10 years, based on PITX2 methylation below a certain "good prognosis" threshold. Those patients designated as having a poor prognosis based on PITX2 methylation exhibited a 43 percent chance of experiencing 10 years of metastasis-free survival.

The company plans to incorporate one or two other markers with PITX2 in the final version of its test.

Previously, the company had tested its markers in tamoxifen-treated patients and untreated patients. The test's primary competition in the marketplace, Oncotype Dx, is intended for use on patients who have had node-negative, estrogen receptor-positive breast cancer, without restrictions on the type of adjuvant therapy they received.

Clinicians who use such cancer prognostic tests may decide to use more aggressive chemotherapy on patients who seem likely to have a poor prognosis — those in whom metastatic breast cancer is likely to recur within ten years.

In six studies of its prognostic biomarkers, Epigenomics has evaluated around 2,000 patient samples, Oliver Schacht, the company's CFO, told Pharmacogenomics Reporter this week. The current study represents the first that Epigenomics has conducted outside a partnership with Roche, which the molecular diagnostics giant cancelled in late January.

The breast cancer diagnostic follows immediately behind the development of the firm's prostate cancer prognostic assay, said Schacht. Epigenomics intends to conduct its pivotal clinical trial for the breast cancer prognostic next year, with results ready in 2008, he said. "We believe that these tests are at least Class II, if not Class III medical devices, so we're aiming for the FDA route." The company will be meeting with the agency during the first half of this year, he added.

Both tumor-classification tests determine prognoses with a recurrence score similar to that used by Oncotype Dx, and both require a tissue sample rather than blood, said Schacht. The company is also working on two tests using blood samples for both indications, but these tests depend on different markers, he said.

Genomic Health is generally praised for the level of clinical validation through which it has put its Oncotype Dx beast cancer prognosis, and any rivals will likely be judged as much on that aspect of a new test as any other. "There is no doubt that they have set a clear standard" that Epigenomics is trying to follow with the validation of its test, including working with nine clinical collaborators who publish the results of its validation studies, said Schacht.

The company had never intended to follow the CLIA route to making its test available for the clinic, as Genomic Health has done with its breast cancer diagnostic, and it sees the recent FDA request to meet Genomic Health to discuss Oncotype Dx's regulation as a corroboration of its approach, said Schacht. "At the same time, we always keep the option open that we could offer this — before we get FDA approval — in a CLIA-certified lab, either our own or a reference laboratory," he said.

The CLIA route limits the kind of claims a manufacturer can make about its test, he added.

Epigenomics was left to develop the breast cancer recurrence test on its own after Roche released to the firm its rights to develop the assay, which the two had been working on jointly since September 2002. Roche also backed out of an alliance with Epigenomics to develop the prostate cancer prognostic test that the companies signed in 2003.

Roche would have taken on the responsibilities associated with regulatory filings and clinical development, according to the companies' agreement.

Neither Roche nor Epigenomics would comment on Roche's reasons for pulling out of the projects.

The companies continue to work together on blood-based tests for early detection of colon, prostate, and breast cancers, said Schacht in February.

— Chris Womack ([email protected])

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