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Almac Diagnostics Expands Biomarker Discovery Service with XCel Array


By Justin Petrone

Almac Diagnostics last week launched its Xcel array for biomarker discovery within multiple disease areas. The new chip, based on Affymetrix's GeneChip platform, is intended for use in studies where cross-disease compatibility is important, an attribute that Almac calls a "notable advantage" for its pharmaceutical customers.

The Xcel array contains 92,000 transcripts and is optimized for use with formalin-fixed, paraffin-embedded tissue. It complements a suite of Disease-Specific Arrays for breast, ovarian, colorectal, lung, and prostate cancer studies Almac has introduced in recent years.

"This is an optimal array for biomarker discovery in that it really includes everything," said Michael Sloan, vice president of business development at Almac Diagnostics. "It has the most significant content from all of our DSAs and it works with FFPE," he said. "It’s a really cracking tool for biomarker discovery, and we are already using the array internally."

Sloan spoke with BioArray News during a visit to Almac's headquarters in Craigavon, Northern Ireland, last month. During the visit, Almac also provided an update on its plans to bring US Food and Drug Administration-cleared, microarray-based tests to market.

Almac Diagnostics was founded as ArraGen in 2003 and rechristened ArraDx two years later before subsequently being incorporated into the Almac Group. In addition to Diagnostics, the Almac Group maintains Clinical Services, Clinical Technologies, Pharma Services, and Sciences divisions, and caters to pharmaceutical companies as an integrated resource that can work with them from biomarker discovery through compound synthesis and drug production.

Philip Diamond, vice president of marketing development at Almac Group, told BioArray News that the bulk of Almac's business is derived from its Clinical Technologies and Clinical Services, though Almac Diagnostics has been contributing to the firm's growth. Diamond declined to break out sales figures for Almac Diagnostics, however.

While Almac Diagnostics has been developing its own GeneChip-based tests for eventual commercialization, the company has increasingly benefited in recent years from partnerships with big pharma for biomarker discovery projects and companion diagnostics work. In the past year, for instance, it has announced such deals with Merck, Lilly, and Pfizer (BAN 4/13/2010).

Most of Almac's work with pharma so far has made use of its DSAs and quantitative PCR platform. What the firm lacked, though, was a more general tool for biomarker-discovery projects. According to the firm, the new chip addresses this issue.

"We needed something that could be used across cancers and that could provide comparable data," said Richard Kennedy, vice president of experimental medicine at Almac. "The beauty [of the XCel array] is that it has the best content of all generic arrays," Kennedy told BioArray News in Craigavon. He said that Almac will continue to use its DSAs for specific disease studies, but that the XCel is the "logical array to use if there is no DSA available."

Austin Tanney, scientific liaison manager for Almac Diagnostics, said this week that XCel rounds out the menu of arrays the firm has developed for use in biomarker discovery work and that no new DSAs are planned.

Tanney told BioArray News that Almac developed the new chip to provide a platform for biomarker discovery in multiple diseases and where more than one indication is being considered. "This is of particular interest in the development of companion diagnostics for multiple indications," he said. In addition, the firm believes the Xcel chip is "suitable cancers for which we have not developed a DSA and it is suitable for diseases other than cancer."

Focus on FFPE

According to Tanney, the array was developed from a combination of public database information and in-house sequencing data, and contains "comprehensive coverage of well-known and annotated transcripts, in addition to a significant amount of proprietary information."

The tool's "key advantage," though, is its ability to work with FFPE samples, Tanney said. Through various partners, Almac maintains access to around 10,000 FFPE tumor samples, a resource that the company is keen to exploit in its companion diagnostics work.

"We have focused on the 3' end of the transcript in the design, using 3' sequencing data, confirmed poly-adenylated public sequence data and 3' focused probe design," said Tanney."Obviously, with the FFPE optimization of the platform, there is even greater advantage in projects which involve formalin-fixed tissues," he said.

According to Tanney, this FFPE focus is "very important, particularly in oncology," and allows Almac to carry out retrospective analysis and to "discover biomarkers that can be developed into tests which do not require changes to current clinical practice."

Almac has not yet used the XCel in any projects involving its pharma clients, but has used it internally. "All work to date has been on in-house projects," Tanney said. "However, we have already had a lot of interest in the platform and we are about to start several customer projects," he said.

Colorectal Test Advances

While Almac expands its portfolio for biomarker discovery and companion diagnostics work, the company is also moving ahead with its plans to bring a GeneChip-based test to market.

Furthest along in its pipeline of diagnostic assays is a test for colorectal cancer recurrence. Almac has been in discussions with the FDA for three years concerning the regulatory path for its assay, which relies on a prognostic gene signature to predict relapse in colorectal cancer (BAN 5/29/2007). The firm had previously said the test could be available for clinical use in the US by as early as 2008.

Almac's Sloan last week updated that forecast by predicting that it could receive 510(k) clearance by early next year. He said that the colorectal cancer test is currently entering a final validation study, and is working with around 20 different centers worldwide to obtain to support its submission.

In addition to its colorectal cancer test, Almac has a second assay for lung cancer in development. The test, which provides an early-stage prognostic signature for patients with early non-small-cell lung cancer, is a "priority" for the company, Sloan said, but stressed that it is in the "early stages" of development. Almac previously discussed the development of its lung cancer test two years ago, when it announced a partnership with 15 centers in the UK, US, Ireland, and Italy to develop the signature (BAN 8/19/2008). At that time, it predicted the lung cancer test could reach the market by this year.

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