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Claremont Bio Wins $3M Phase II SBIR Grant to Further Develop Sample Prep Cartridge, MDx for C. Diff

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Claremont BioSolutions has been awarded a three-year, $3 million grant from the National Institute of Allergy and Infectious Diseases to continue developing its fully integrated and portable point-of-care assay system for detecting Clostridium difficile infections and contamination.

Claremont will initially use the award, a Phase II Small Business Innovation Research Grant, to further optimize and commercialize its disposable sample prep cartridge, which it claims can extract relevant nucleic acids in less than five minutes and in two to three steps.

The company then intends to integrate this cartridge with a detection module running one of two isothermal amplification techniques it is developing in partnership with the Keck Graduate Institute and PATH, Bruce Irvine, principal investigator on the project and chief technology officer at Claremont, told PCR Insider this week.

In addition, Irvine said that by the third year of its project, the company plans to work with researchers at Beth Israel Deaconess Medical Center and Pomona Valley Hospital Medical Center to test the clinical feasibility of the device.

Spun out of the Keck Graduate Institute in 2006, Claremont has since been working closely with KGI to develop and commercialize a variety of nucleic acid sample prep technologies, and more recently has also begun investigating how to integrate those technologies into molecular diagnostic systems.

In April, PCR Insider wrote about some of the molecular testing technologies being developed by Claremont and KGI collaborator Angelika Niemz, including the C. difficile assay and tests for multi-drug-resistant tuberculosis and herpes simplex virus (PCR Insider, 4/26/2012).

Of these tests, Claremont has focused most heavily on commercializing its C. diff assay, and in 2009 was awarded a two-year, approximately $600,000 Phase I SBIR grant from NIAID to develop its integrated molecular testing device to detect the TcdA gene, TcdB gene, and TcdC point mutations of C. difficile from patient stool samples to diagnose infection, and from environmental swabs to curtail C. diff-related hospital acquired infections.

Common to all of the molecular tests under development at Claremont and KGI will be a sample prep module that more efficiently automates Claremont's commercial PureLyse product for cell lysis and DNA extraction.

The prototype module, which Claremont will continue to refine under the new Phase II SBIR grant, uses a combination of mechanical lysis and chemical lysis to disrupt bacterial cells and extract and purify DNA.

"The current version … can be operated either with a disposable syringe or pipette," Irvine said. "There is a very tiny motor embedded in the disposable cartridge, the same motor that makes your cell phone vibrate. They're produced in high volume, therefore they are very cheap."

This motor helps drive mechanical lysis using bead technology, and those same beads are also used to bind nucleic acid.

Further, for the C. difficile test, which must be able to overcome the PCR inhibitors commonly found in stool samples, Claremont's device will feature some proprietary extraction chemistry as well as a filter that removes large particles from the sample and background DNA before cell lysis; and also removes anionic polysaccharide inhibitors. "We also address another category of inhibitors in the extraction protocol, but I don't want to disclose what inhibitor and what method that is before we lock down the IP on that," Irvine said.

The cartridge is expected to be able to reduce nucleic acid sample prep down to two or three steps, in around three to five minutes depending on the protocol, Irvine said. While the value of this is obvious for a point-of-care diagnostic platform, Claremont believes it may also benefit molecular biology researchers, who currently generally use time-consuming, manual processes to extract DNA.

"We're doing this in modular steps so the automated sample prep module will be an independent product itself," Irvine said. "We're very excited about this, because we realized that we can give customers complete automation in five minutes long before the final [integrated diagnostic] product ever goes to market."

Irvine also noted that if Claremont can successfully develop its device for stool samples, it should work to prepare nucleic acids from a wide variety of samples, since stool "is definitely a worst-case scenario [and] one of the more difficult samples to deal with."

Claremont then plans to embed its automated PureLyse cartridge with its so-called OmniValve fluidic technology, creating a valve with up to six ports connecting the lysis and extraction cartridge to other chambers and integrate the DNA extraction with the other test steps, including amplification.

For amplification, Claremont will "pursue a pair of isothermal amplification schemes and then have a feasibility test to decide which one to stay with." KGI is developing one isothermal method, and Seattle-based non-profit research institute PATH is developing the other. "They’ll be sort of dueling in their efforts to optimize isothermal amplification," Irvine said. As such, KGI's Niemz and PATH's David Boyle are listed as co-PIs on the Phase II SBIR grant.

Finally, for detection, Claremont hopes to use its proprietary portable fluorometer, called FluoriSense. "The idea is to make the disposable … and the instrument low cost," Irvine said, though he declined to detail how the ultimate cost of the platform would compare to other current molecular testing platforms for C. diff.

If all goes as planned, in the third year of its project Claremont plans to work with Beth Israel Deaconess — specifically the laboratory of GI infectious disease expert Ciaran Kelly — as well as nearby Pomona Valley Hospital Medical Center "to do a beta feasibility test" on the integrated device, Irvine said.

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