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Foundation Medicine to Develop Sequencing-Based Comprehensive Cancer Test for Novartis


By Turna Ray

Foundation Medicine's first collaboration
with a large pharmaceutical company, Novartis, will center on developing a sequencing-based comprehensive cancer analysis test for use in the pharmaceutical firm's clinical trials.

"The test being developed already is operational in a research test mode, and we aim to achieve our clinical and regulatory certifications," Alexis Borisy, Foundation Medicine's CEO, told PGx Reporter via e-mail. "This test will look comprehensively at several hundred genes by deep sequencing (capturing all mutations, insertions, deletions, translocations, copy number variation, etc.) at an extremely high sensitivity, specificity, and reliability."

The financial terms of the deal between Novartis and Foundation Medicine were not disclosed.

The collaboration will kick off with a pilot program in which Foundation Medicine's existing comprehensive cancer test panel will be enhanced for "Novartis' needs."

"The aim here is to create a clinical-grade, regulatory-grade, robust, real-world routine clinical use product," Borisy said. If the pilot phase is successful, the partners may advance the test for commercial use.

Foundation Medicine, which launched last year with $25 million in Series A financing, is a personalized medicine-focused company that aims to apply next-generation sequencing to individualize cancer treatment (PGx Reporter 04/21/10). The company has previously said that it plans to develop "comprehensive" cancer molecular diagnostics, but is platform agnostic when it comes to using a specific type of sequencing technology.

Neither Borisy nor the company's website provided any specific details regarding the technology base underlying the cancer test under development. Foundation Medicine's website notes that its comprehensive cancer genomics laboratory tests "are in development and not yet available for clinical use."

By working with a drug company to further develop its test, Foundation Medicine is hoping to speed the pace of drug development in oncology and have a positive impact on patient recruitment in clinical trials.

"One could imagine how pharma companies could be natural early adopters, for use in their clinical trials, of the comprehensive clinical cancer genomics test being developed by Foundation Medicine," Borisy explained. "By use in their trials we do not mean a retrospective, research orientation, but rather in-line clinical incorporation into trials."

The fact that Novartis will be using Foundation Medicine's test to run clinical trials aimed at personalizing cancer treatment, and ideally, picking out the best responders to a therapy, "could increase the interest in physicians participating in those trials, patients' willingness to enroll in trials that are a good match for what has gone wrong in their specific cancers, as well as generate much useful data for the pharma company," Borisy added.

The partners did not disclose the specific drug development program for which Novartis plans to use Foundation Medicine's test.

Borisy couldn't provide too many specifics about the pilot program with Novartis beyond the fact that it is a "broad-based program" at the drug firm.

Novartis' decision to use sequencing technologies in its drug development programs is in line with other large pharmaceutical firms, such as Merck, GlaxoSmithKline, Johnson & Johnson, and Pfizer, that have said they are using sequencing strategies for early biomarker discovery and for patient stratification in clinical studies.

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