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Almac's Disease Specific Array Yields Multi-gene Breast Cancer Chemotherapy Response Test


A new assay that can be used to gauge a breast cancer patient's response to chemotherapy is described in a new Journal of the National Cancer Institute paper.

The authors claim that the 44-gene signature can predict the benefits from DNA damage-based drugs, including commonly used anthracycline- and cyclophosphamide-based chemotherapy regimens. The signature was developed using Almac Diagnostics' Breast Cancer Disease Specific Array (DSA), in collaboration with researchers from Queen's University Belfast and the Mayo Clinic in Rochester, Minn.

Almac in November announced that it had licensed the signature to Genomic Health for commercialization. Richard Kennedy, medical director at Almac Diagnostics, a business unit of the Craigavon, Northern Ireland-based Almac Group, told BioArray News this week that his company and Genomic Health would advance the signature toward that goal in new studies.

According to Kennedy, Genomic Health will "further develop, validate, and subsequently commercialize" the test. "Such a test would be particularly useful for high-risk breast cancer patients who are eligible for chemotherapy based on their Oncotype DX score," Kennedy noted.

Genomic Health's Oncotype DX breast cancer test assesses the risk of recurrence for breast cancer and is used to predict response to chemotherapy. The firm also offers Oncotype DX tests for colon and prostate cancer, but the breast cancer test is its top-selling product.

To develop the assay, Almac used its Breast Cancer DSA to analyze patient samples and identified a molecular subgroup with a deficiency in DNA damage repair, which it labeled as DNA damage repair deficient (DDRD). Almac then developed a 44-gene classifier capable of prospectively identifying this molecular group in patient tumor samples.

Almac initially validated the DDRD signature in a neo-adjuvant breast cancer cohort. According to the company, in the neo-adjuvant setting the assay predicted complete pathologic response with an odds ratio of 3.96, meaning those patients that were DDRD positive were almost four times more likely to respond to treatment compared to patients that were DDRD negative.

In the adjuvant setting, a DDRD-positive result predicted five-year relapse free survival with a Hazard Ratio 0.37 compared with test negative patients, Almac said.

Upon licensing the new signature, Genomic Health made a $9 million upfront payment, which it said it expected to expense in the fourth quarter. It also said it would make additional milestone payments upon certain clinical and commercial endpoints being met, and if the test is commercialized, Genomic Health will pay additional royalties to Almac.

The Breast Cancer DSA is based on an Affymetrix-manufactured chip that contains 60,000 transcripts relevant to breast cancer. Almac Diagnostics has developed other DSAs for colorectal, ovarian, lung, and prosate cancer, and has advanced its own predictive tests on the chips in addition to making them available as research tools for its partners. Almac also has developed a more generic, cancer-focused array called Xcel, that Affymetrix distributes as a catalog chip globally. All of Almac's arrays are designed to be able to capture information from degraded, formalin-fixed, paraffin-embedded samples.

In a statement, Paul Harkin, Almac Diagnostics' president and managing director, called the JNCI paper a "significant milestone" for the company as it transitions its assay into clinical use.

Though the new signature was developed using arrays, it is not likely to make it to the clinic as an array-based test. Kennedy said that since the "DDRD subgroup is a biology," it is "therefore amenable to different platforms," meaning the platform could change. And Genomic Health spokesperson Emily Faucette told BioArray News that it is the company's intention to move the licensed signature over to a real-time-PCR platform. Genomic Health's flagship assay, Oncotype DX, is also run using RT-PCR.