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Stepping into Diagnostics, Compendia Lends Informatics Expertise for AltheaDx's Breast Cancer Assay


By Uduak Grace Thomas

Compendia Biosciences has taken its first step into the diagnostic market under a partnership with AltheaDx, a San Diego-based diagnostic development and testing company.

The firms recently announced their intent to pool their expertise to focus on cancer biomarker discovery and the development of tests to predict patient outcomes in clinical trials. The first product under the partnership is a real-time PCR-based Breast Cancer Segregation Panel Assay that measures 96 genes that Compendia identified via a meta-analysis of cancer genomic data from more than 5,000 samples.

Under the terms of the partnership, AltheaDx will process and analyze the samples in its CLIA- and GLP-certified laboratory, while Compendia will handle downstream data analysis and statistical correlation to patient outcomes in clinical trials.

Financial details of the partnership were not disclosed.

Although Compendia has worked with pharmaceutical companies in the past, this partnership marks the company's first tool for "companion diagnostics for drug development," John Freshley, chief business officer for the company, told BioInform.

He said that Compendia is bringing its "cancer genomic expertise" to the partnership, including its Oncomine database of more than 50,000 genomic profiles, which it is using to "identify the genes most robustly associated with various disease states" as part of the assay-development process.

"For each disease that we wish to do a tumor segregation panel assay ... we have taken dozens of datasets from different cohorts and identified key biological variables and genes that measure those variables," Freshley explained. "And then, we [put] those genes that perform well ... onto the assay.

"What that will allow us to do is measure in each patient the key biological variables of the disease," he continued. "If we use that assay in association with a clinical trial, we believe that those variables will be particularly informative when trying to understand patient response and resistance."

Matthew Gorovoy, AltheaDx's associate director of corporate development, told BioInform that although his company has worked on projects related to inflammation and neurodegenerative disorders, "oncology is our main focus." He added that Compendia's oncology software and database "complement" AltheaDx's offerings.

By running the segregation panels on samples, pharmaceutical companies can stratify patients based on their gene-expression patterns, Gorovoy explained. This information would be useful in identifying cancer therapies that would be most effective for particular patients, or for selecting participants in clinical trials, he said.

More than the size of the market, the partners chose to address breast cancer first to fulfill an "unmet need" Gorovoy said.

"There is a lot of information available ... from genetic analysis; at the same time that information may be unstructured and may not be useful for researchers in pharma and biotech," he explained. "That’s what we offer with our partnership. ... We are mining the information and offering a much higher level of analysis."

Gorovoy said that it is "possible" that AltheaDx will seek FDA approval for the tests it is developing under the partnership, but "not in the near future."

The breast cancer segregation assay is currently marketed by both companies under a joint direct sales effort.

The companies plan to launch a colorectal cancer panel next year and Gorovoy said that the partners may develop a lung cancer panel after that.

Freshley also said that the partners plan to publish a paper that describes the meta-analysis and the methods used to identify the gene signatures as well as a clinical validation of the approach in the second half of 2011.

From Biomarker Discovery to Clinical Applications

While the emphasis still is on oncology at Compendia, Freshley said that in the last three to four years, the company's focus has shifted away from target discovery and validation and is moving towards clinical development and applications.

He noted that the company has been working with several pharmaceutical companies in cancer genomic biomarker discovery and in the applications of these biomarkers. However, he said, "I think what we are finding is that ... slowly but surely, now we spend more of our time in the early clinical phase working with our customers."

The primary need within that space, according to Freshley, is to identify biomarkers and find ways to translate them to clinical utility, which he said is "what we do" at Compendia.

As the company adjusts to address the demands of clinical applications, Freshley said that both the software and services arms of Compendia are "growing well," though the software business is the larger of the two.

He noted that the services arm is "feeding" the software business because "it teaches us the tools that our customers need best," he explained. "We do some services and then we build the tools and then we sell the tools so it's been a nice cycle."

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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