By Monica Heger
This story, originally published Aug. 16, has been updated to clarify information about the performance of the company's tests.
Pathogen sequencing company Pathogenica is developing its first product — a sequencing-based diagnostic for human papillomavirus — which it expects to launch in 2012 as a US Food and Drug Administration-approved kit.
The company, founded in 2009 and based in Cambridge, Mass., has evaluated the tests on the Ion Torrent PGM, but said that the assays are "platform agnostic," and with minor adjustments can run on any next-generation sequencer.
The company is also developing sequencing-based tests to measure viral load and drug resistance in HIV patients and hepatitis C patients, but has not provided an expected launch date for those tests.
At the Next Generation Sequencing and Genomic Medicine Summit in San Francisco this month, Graeme Doran, Pathogenica's chief scientific officer, gave an overview of the tests and the company's technology.
The company's proprietary capture technology, DxSeq, is key to its tests. Pathogenica has designed more than 75,000 probes to target specific pathogens within a sample containing both human DNA and viral or microbial DNA.
The capture and library construction steps are combined in one tube and take under three hours, enabling a turnaround time of 12 hours from "blood sample to outcome," said Doran.
The probes "reduce the number of processes and hands-on time, and also allow for multiplexing," Pathogenica's CEO Yemi Adesokan told Clinical Sequencing News in a follow-up interview.
In addition, the probes enable the sequencing of viral DNA present at very low copy number, said Doran. The company has demonstrated that its technology can enrich microbes and pathogens from human tissue samples, depleting human DNA to less than 0.1 percent of sequence reads.
The company has developed a highly multiplexed pool of different probes to target HPV. Testing the probes with the PGM on 21 clinical samples from Brigham and Women's Hospital, they demonstrated multiplexing several patient samples together and identification of HPV subtypes with 100 base reads.
"We were able to capture specific subtypes for each sample," Doran said, as well as "identify multiple infections" and "identify and confirm the subtypes." Using traditional PCR and Sanger sequencing, the team confirmed 100 percent of the findings.
Pathogenica plans to publish the results of this study in a peer-reviewed journal.
The company has not settled on a price for its test, but said it would be comparable to existing tests. Additionally, Adesokan said that he expects it to be reimbursed by payors.
Pathogenica plans to provide HL7-compatible reports that integrate with existing health information technology systems, but also will allow access to reports through a cloud-based service that will allow clinicians to determine whether a specific pathogen is present at a clinically significant level.
The market for HPV molecular testing has become increasingly crowded in recent years as it has gained favor as an approach to identify women at higher risk of cervical cancer.
Once it launches its test, Pathogenica will compete with a number of companies including Hologic, Qiagen, Roche, and Gen-Probe. Roche recently received FDA clearance for its PCR-based HPV test, which, according to the company, is the only FDA-approved test that enables HPV 16 and 18 genotyping concurrently with high-risk HPV testing.
Gen-Probe has also filed a premarket approval submission with the FDA for an HPV assay that runs on its Tigris nucleic acid amplification platform.
Doran said that using next-gen sequencing to test for HPV would allow more accurate detection of multiple infections and help reduce the number of false positives that other tests pick up.
Pathogenica is also designing assays that will detect drug resistance in HIV and HCV. Doran said that with the company's DxSeq probes and next-gen sequencing, HIV genotyping could be reduced from three to four weeks to just a few days, which would be particularly important for deciding whether to switch a patient's therapy, and what the correct treatment would be.
Doran said the assays could be used in clinical trials to monitor the emergence of drug resistance, to monitor drug response, by "identifying changes in population before and after therapy," he said.
While the company is currently testing all its assays on the PGM, Doran said that they could be run on any sequencing machine. Already, said Adesokan, academic researchers, pharmaceutical companies, and clinical labs have been using the kits for research purposes.
The company is also working on assays targeting methicillin-resistant Staphylococcus aureus, Escherichia coli, and different types of fungal infections, and is looking to collaborate to develop assays for surveillance of both clinical and environmental samples and for screening food and water.
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