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DoD Awards IntegenX up to $14.8M to Develop Integrated 'Sample-to-Sequence' System for Pathogen ID

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By Ben Butkus

Sample prep specialist IntegenX has been awarded a contract worth up to $14.8 million from the US Department of Defense to develop an integrated sample-to-sequence system to rapidly detect and identify genetically engineered, medically relevant, and emerging pathogens from environmental samples.

Under the contract, IntegenX will use its Universal Sample Preparation Module, or USPM, to purify DNA from pathogen targets contained in complex environmental matrices and present the purified material to other IntegenX modules for library construction, amplification, and next-generation sequencing.

IntegenX, based in Pleasanton, Calif., said that it will be the primary contractor for the first phase of the project, which is funded through DoD's Defense Threat Reduction Agency, and is worth $2.8 million over the next several months.

However, assuming IntegenX achieves certain undisclosed milestones, the contract may be worth an additional $12 million over 18 additional months. At the end of that time, the DoD or DTRA can acquire a certain number of the final system for deployment around the world, Howard Goldstein, IntegenX's executive vice president for commercial affairs, told PCR Insider this week.

IntegenX, previously called Microchip Biotechnologies, developed its USPM technology about four years ago under previous funding from the US Army, DTRA, and Defense Advanced Research Projects Agency, Goldstein said.

The goal of that project was to develop a system that law enforcement agents could use to purify DNA from a biological sample taken from a criminal suspect so that it could be compared to reference databases.

"Today that process is very slow, and takes eight to 10 days, several people, and about $2 million worth of equipment," Goldstein said. "We've put it into a [2-cubic-foot] box that will cost about $100,000, and will give an answer in two hours or less."

Based on the successful completion of that project, DoD and DTRA "became interested in our proposal to [adapt that to] an environmental sample, whether it's air, water, or soil, and which might have a bioengineered pathogen in it," Goldstein added.

To that end, IntegenX will put its USPM technology at the front end of a system comprising existing DNA library construction, PCR amplification, and next-generation sequencing modules.

"We're going to integrate technologies, some of which are out there, that will take in a sample, prepare it for next-gen sequencing, sequence it in a fast way, and essentially give the user within a two- to four-hour window information about what the organism is, should we treat it, is it something we have to worry about, [or] is it pathogenic," Goldstein said.

Goldstein said that IntegenX is working with companies in the PCR and next-gen sequencing arenas to develop the system, but declined to disclose their identities, citing confidentiality agreements. "We've been asked by DTRA to take certain technologies that are either commercially available or that they've been testing, and integrate them using our technology," Goldstein said.

IntegenX's ability to integrate these various modules into a complete sample-to-answer system is enabled by a patented technology called microscale on-chip valves, or MOVe, developed in the laboratory of Richard Mathies at the University of California, Berkeley, and exclusively licensed to IntegenX.

The MOVe technology is used to automate and miniaturize complex chemistries, according to the company's website. It is enabled by a flexible polydimethylsiloxane membrane placed between etched glass or molded plastic layers. The bottom layer is connected to an external conventional-scale pneumatics system. When a vacuum is applied to the pneumatic displacement chamber, the normally closed PDMS membrane deflects from the valve seat and the valve opens.

Operating three or more of these valves creates adjustable flow in any desired direction through pressure changes similar to a diaphragm pump, enabling advanced microfluidic applications, according to the company.

"That technology gives us the capability of integrating a very fragmented kind of instrumentation," Goldstein said. "The way you flow material from one subsystem within a workflow — we can essentially do it at a minimal volume and therefore have no dilution or change in the sample. So we have exquisite control over moving these samples around. That's what allows us to glue these various parts together."

The MOVe technology also forms the basis of several other IntegenX platforms for sample preparation either on the market or in development.

First, the company's only commercially available product, the Apollo 100, integrates the MOVe technology to prepare samples for Sanger sequencing. "That system is designed for people who already have DNA sequencing devices that they're using," Goldstein said. "It automates the workflow that precedes the sequencing, from sample to dye attachment to getting the sample in the appropriate form so it can be injected automatically onto an automated Sanger system, typically an [Applied Biosystems] 3130 or 3730. Those are now in the field and selling well."

In addition, IntegenX is developing the Apollo 200 system, an integrated sample-prep system for human DNA Identification targeted at law enforcement agencies. According to the company's website, it is developing an 8-channel version of the Apollo 200 system and is seeking development partners. It plans to commercialize this system next year.

And lastly, the company is working on the Apollo 324 library-preparation system for next-gen sequencing. This product, for which IntegenX is also seeking collaborators, will enable researchers to process between eight and 96 samples in parallel using fewer reagents than typical DNA library-generation methods. IntegenX will be unveiling an early version of this product in November at the American Society of Human Genetics meeting in Washington, DC.

"All our products that do any sample prep from raw sample use this technology module that we created," Goldstein said. "And we've built it so it can be treated like an erector set or building blocks. We can essentially cut and paste."

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