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Pathogenica Bets on Next-Gen Sequencing for Fast, Multiplexed Pathogen Detection

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By Julia Karow

This article was originally published June 30.

Harvard Medical School spinout Pathogenica is developing infectious disease pathogen detection assays that use targeted next-generation sequencing and promise to be faster and more multiplexed than existing assays.

The company, which is still exploring various next-gen sequencing platforms, plans to deploy its assay panels — targeted at different types of diseases — in a CLIA-certified lab setting next year and to start testing them in clinical trials. It wants to launch an FDA-approved product by the end of 2012.

Based in Cambridge, Mass., with part-time consultants on the West Coast, Pathogenica was founded a year ago by Harvard Medical School professor George Church and Yemi Adesokan, a former postdoc in his lab.

Besides Church, the firm's scientific advisory board includes Stanford Genome Technology Center director Ron Davis; University of California, San Diego professor and former Church postdoc Kun Zhang; Columbia University professor Ian Lipkin; and Harvard Medical School professor Andrew Onderdonk.

The company, which licenses intellectual property for some of its assays from Harvard, has raised almost $500,000 in angel investment and is currently talking to venture capital firms on both coasts, with the goal of raising up to another $3 million by the end of this year. It also has pending grant applications with the National Institutes of Health and the Defense Advanced Research Projects Agency.

Its assay panels will probe for about 100 pathogens per clinical sample, targeting specific regions within each pathogen's genome, for example those responsible for drug resistance. The company uses a proprietary capture method with up to 75,000 probes, according to its website, to enrich the target regions, followed by sequencing, and is developing software for reporting the results to clinicians.

The technology is not restricted to any sequencing platform, and at the moment, company researchers run their assays on both Sanger and Illumina platforms, outsourcing their sequencing needs to several undisclosed facilities. But the firm is keeping an eye on new sequencing platforms under development, especially those with a lower throughput per run and shorter run times than existing next-gen platforms, such as Ion Torrent, GnuBio, or Pacific Biosciences.

"Our technology doesn't really need that type of a high-throughput platform," Adesokan told In Sequence. Rather than data produced at the rate of a fire hydrant, "we are looking for more of a water fountain approach," he said.

Pathogenica is looking to partner with sequencing platform developers to develop assays for their instruments, he said, and is currently in discussions with several of them. "We would like to be an application that goes on any of these platforms," he said.

In addition, it might partner with an existing CLIA-certified lab to commercialize its assays early next year.

An example of a possible use of the technology is to help diagnose meningitis. Right now, Adesokan said, it takes at least four days to detect the pathogenic agents by culture-based assays, and about 20 pathogens could cause the disease. "Our technology could probe for all those pathogens in one go" at comparable sensitivity and specificity, and within less than 24 hours, he said.

Compared to PCR, which is difficult to multiplex, Pathogenica's technology will be able to target more pathogens at a time with no increase in cost, he said.

And while he claimed there is currently no competitor using a sequence-based approach to detect infectious disease pathogens, the company will most likely compete with Cepheid, which markets real-time PCR testing systems for infectious disease diagnostics, and Gen-Probe, which recently invested in Pacific Biosciences.

Pathogenica might also run into BioMérieux, which said earlier this year that it plans to develop a next-gen sequencing-based in vitro diagnostics platform with first applications in cancer and infectious disease diagnostics (IS 4/27/2010).

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