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Following Acquisition, Roche Plans to Integrate CAPP Medical into Sequencing Unit

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NEW YORK (GenomeWeb) – Roche plans to integrate CAPP Medical, the Stanford University spinout it acquired earlier this month for an undisclosed amount, into its sequencing unit.

A Roche spokesperson told GenomeWeb that one undisclosed CAPP Medical employee will join the Roche Sequencing Unit in Pleasanton, Calif., while several others will consult for the company. This strategy appears to differ from that for other recent acquisitions, for example, of Ariosa Diagnostics and Genia, which Roche is operating as standalone units.

The spokesperson confirmed that CAPP Medical's founders are Max Diehn and Ash Alizadeh, both group leaders at the Institute for Stem Cell Biology and Regenerative Medicine at Stanford School of Medicine, and Ashok Kirshnamurthi, CAPP Medical's CEO from its inception in October 2013 until Roche's acquisition this month.

Alizadeh told GenomeWeb that CAPP Medical, which was based in Palo Alto, had been operating in stealth mode and had disclosed few details about its funding and research prior to the acquisition. He declined to provide further information about the company.

However, a year ago, Diehn's and Alizadeh's groups published a paper in Nature Medicine in which they presented CAPP-Seq, short for Cancer Personalized Profiling by deep Sequencing, a sensitive and inexpensive method for detecting and profiling circulating tumor DNA from cancer patients. The Roche spokesperson confirmed that CAPP Medical was developing the CAPP-Seq method.

The method relies on identifying highly mutated genomic regions for specific cancer types bioinformatically based on existing data, capturing those regions in patient blood samples, and sequencing them with high coverage.

In their paper, the researchers tested CAPP-Seq on samples from non-small cell lung cancer patients. They were able to detect ctDNA in all patients with stage II to IV disease and in half of patients with stage I disease. CtDNA levels correlated well with tumor volume and were able to distinguish between residual disease and treatment-related imaging changes. Also, ctDNA levels allowed the researchers to assess treatment response earlier than radiographic imaging.

According to Diehn's website, the method "is extremely sensitive and specific and was designed to apply to the vast majority of patients with a given cancer type, without the requirement for patient-specific optimization."

Since last year's publication, the group has extended the method to a variety of other tumor types besides lung cancer, according to the website, and is working on clinical trials to establish the clinical utility of ctDNA detection in different cancer types. In addition, it is exploring ctDNA for cancer screening and early detection.

Last October the US Patent and Trademark Office published a patent application by Diehn, Alizadeh, and two others on the identification and use of circulating tumor markers. The application, No. 20140296081, covers "methods for creating a library of recurrently mutated genomic regions and for using the library to analyze cancer-specific and patient-specific genetic alterations in a patient." These methods "can be used to measure tumor-derived nucleic acids in patient blood and thus to monitor the progression of disease," as well as for cancer screening.

Roche declined to comment on how specifically it plans to apply CAPP Medical's technology, but it may decide to use the CAPP-Seq method as part of its collaboration with Foundation Medicine. Earlier this year, Roche and Foundation said they were going to co-develop a ctDNA blood test, the first version of which they plan to launch by the end of this year, for use by Foundation's biopharmaceutical partners.

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