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Novartis Research Group Aims to Use NGS, Other Technologies to Develop Personalized Cancer Dx

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Novartis is launching a research group that will use next-generation sequencing, proteomics, and other technology to develop diagnostics to stratify cancer patients into existing clinical trials, to identify new markers for future drug development, and to commercialize assays through its diagnostic group Genoptix.

The Next Generation Diagnostics group will include between 35 and 40 people, about half of whom will be recruited by the end of the year, and is aiming to have its first assays function in clinical trials within one year.

Bill Sellers, global head of oncology at Novartis Institutes of BioMedical Research, is spearheading the group and told Clinical Sequencing News that the overall aim is to transition from developing companion diagnostics that are focused on a specific drug toward diagnostics that are specific to the molecular profile of a patient's tumor.

"We're open to all sorts of technologies that are useful in giving a more comprehensive view of the tumor," he said. "Next-generation sequencing will be a significant component, but we're not wedded to a specific technology."

The group will primarily use targeted sequencing strategies, including RNA-seq, exome sequencing, and candidate gene sequencing, said Sellers. "Whole-genome sequencing is still a little expensive to apply at large scale," he said, but it could still be applied to "selected patient samples when interesting clinical results have been discovered but remain to be understood, for example if an RNA-seq or exome sequencing didn't reveal anything."

He said the first task of the group will be to make sure that genomic data is being collected from all patients within Novartis' own ongoing clinical trials. That data will initially be used to do retrospective analyses to better understand the genomic determinants of patient response, he said.

Because the sequencing will be done retrospectively, the data won't be used as an upfront patient stratifier, he said, but instead will be used to generate testable hypotheses for future work.

That data would then be used to develop assays that could be tested for their ability to predict which patients will respond to certain drugs, and "as the assays become more robust and well defined, there is the opportunity to start using the assays to screen patients for entry into our clinical trials," he said.

Eventually, Sellers said, the assays could be shared with the company's San Diego-based diagnostics group Genoptix for commercialization. Novartis acquired Genoptix in early 2011 and the business falls within Novartis Molecular Diagnostics. Earlier this year, Genoptix launched its first sequencing-based test — a targeted panel that runs on the Ion Torrent PGM and detects mutations in BRAF, NRAS, and c-KIT to help physicians guide therapy for metastatic melanoma (CSN 3/28/2012).

Sellers said that the Novartis Next Generation Diagnostics group would be open to developing diagnostics for existing Novartis drugs as well as identifying potential novel drug targets. While the broader, retrospective analyses of clinical trial samples will focus on the "intersection of genomic pathway data with drug response from existing Novartis drugs," because so much data will be generated, new discoveries will be made, and "we'll definitely be looking at that as a new avenue in which we can make assessments about new drug targets."

The sequencing will most likely be done in-house, although Sellers said that the group would be open to outsourcing some of the sequencing work, depending on the robustness of the providers, quality, and sample handling. Additionally, he said that at some point it might become desirable or necessary to do the sequencing within a CLIA-certified laboratory.

Sellers added that he foresees the group collaborating with academic groups that are studying more general problems in oncology. Such collaborations would not be focused on specific Novartis drugs, but rather related to issues such as trying to understand the genetics of response to the standard of care, he said.

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