By Tony Fong
NEW YORK (GenomeWeb News) – Startup pathogen sequencing firm Pathogenica today said that it has received a cooperative research agreement from the US Army Medical Research Institute of Infectious Diseases to develop technologies for the detection of pathogens that could be used as biothreats.
The technologies being developed will be based on Pathogenica's next-generation sequencing-based DxSeq technology. USAMRID will provide data to the company for the design of the biothreat-specific assays. In addition, the Cambridge, Mass., startup is developing host-specific assays for clinical purposes, including assays for microRNA and DNA disease biomarkers.
Pathogenica CEO Yemi Adesokan, who co-founded the company in 2009 with George Church, told GenomeWeb Daily News that the CRADA is for one year and is renewable afterward. He declined to disclose the amount of funding associated with the agreement but said that Pathogenica will have the rights to exclusively license intellectual property emerging from the agreement.
The firm's DxSeq platform uses selective sequencing to detect and assess biomarkers in tissue samples. Using up to 75,000 diagnostic sequencing probes, it allows researchers to read and report on DNA sequences of target pathogens in a sample.
According to Pathogenica, other technologies for detecting pathogens, such as PCR and microarrays, are limited by the fact that knowledge of the pathogen's genome is required beforehand. Because DxSeq uses next-gen sequencing technology, that information is not necessary.
"With the application of our technology merged with sequencing, we can get a view of novel organisms that have never been seen before," Adesokan said.
Compared to PCR technology, DxSeq has the same sensitivity but offers much higher levels of multiplexing, he said, noting that the technology can detect up to 75,000 different substrains of species within a sample, something not achievable with PCR-based methods.
In terms of specificity, the technology can differentiate between species "at even a couple of point mutations," he said, and added that DxSeq is "a lot cheaper" than microarrays because of the drop in the cost of sequencing and because it requires less DNA.
The technology also is platform agnostic, Adesokan noted.
The company has done a proof-of-concept on the DxSeq technology in clinical samples, and for the CRADA it is designing assays against the data supplied by the US Army and then validating it. Pathogenica is developing the platform for a specific biothreat target identified by the US Army, though Adesokan declined to elaborate.
At the end of 2011, Pathogenica hopes to publish results achieved from the CRADA. Adesokan said that the plan is to commercialize the DxSeq technology as a service in mid- to late-2011 and to launch kits in late-2012 or early 2013.
When it launches as a service, Pathogenica plans to partner with an existing CLIA laboratory. But it also plans to seek regulatory approval from the US Food and Drug Administration for its kit diagnostic.