By Ben Butkus
A team of engineers and biomedical researchers from Michigan State University has developed a low-cost, handheld platform that uses a quantitative version of isothermal amplification to measure DNA, RNA, and other biomarkers, including microRNAs, PCR Insider has learned.
The team, which has so far validated detection assays for more than 50 bacterial pathogens on the device primarily for water safety testing, is now working to validate the platform for various cancer and infectious disease applications with an eye toward deployment in resource-poor areas of the world.
As such, the scientists are also seeking industrial partners to help identify potential application areas and support validation studies, Syed Hashsham, a team member and professor in the departments of civil and environmental engineering and microbial ecology at MSU, told PCR Insider this week.
"Because the actual deployment of this device will depend on where it has been clinically validated, and whether we find funding, I'm quite open to about 14 different directions, because for me it is just deciding on which primers to use. I am not tying myself to only one area," Hashsham said.
"Then clinical validation will definitely require more money from industry partners," he added.
The platform, called Gene-Z, is several years in the making, and started out as a handheld nucleic acid analysis platform for identifying pathogens in water. In the mid-2000s, Hashsham helped found an MSU spinoff called AquaBioChip, which licensed the appropriate intellectual property from the university and tried to tackle the water safety market. However, this application was not the low-hanging fruit that it was made out to be by various business consultants, Hashsham said.
"We focused about eight years ago on water [safety], and we basically failed miserably," he said, adding that the company received various design awards for Gene-Z, "but not a single customer. People told us we didn't need [US Food and Drug Administration] approval so it would be [an] easier [market] to penetrate. But … the water industry is not measuring anything not regulated by the [Environmental Protection Agency], so it's more regulated than clinical assays, almost."
Subsequently, the company began exploring other application areas such as plant biology and clinical testing, particularly for infectious diseases. It was after partnering with other scientists in MSU's Institute of International Health that Hashsham and colleagues began to fully understand the potential of their technology in cancer biomarker detection and infectious disease testing, particularly in developing countries.
This in turn spurred the group to combine resources and develop new amplification and detection strategies that would enable the device to do a wide variety of nucleic acid testing for cancer — including miRNA biomarker amplification — cheaply and quickly, a topic that was the subject of a poster presentation earlier this month at the National Institutes of Health's first Cancer Detection and Diagnostics Conference in Bethesda, Md.
The current prototype Gene-Z device is a handheld, battery-operated device featuring software that allows operation with an iPod Touch or Android tablet, and uses microfluidic consumable chips with anywhere from 64 to 1,536 1-mL wells.
The platform allows quantitative isothermal amplification of DNA, RNA, and microRNAs in 10 to 30 minutes; and the researchers speculate that the device could sell for less than $1,000 with the consumable chips costing $2 to $20, depending on the density and application.
Hashsham declined to provide specific details on the novel isothermal amplification method employed by Gene-Z, citing the fact that his research group is currently preparing several manuscripts describing the technology for publication in scientific journals. Similarly under wraps is the group's proprietary method for isothermal amplification of miRNAs
However, he noted that as far as he knew, it would be the first platform capable of measuring isothermal amplification of nucleic acids in real time, thus allowing the same type of quantitative measurements enabled by real-time PCR but at a much lower cost and in a much shorter amount of time.
"Other people have been able to do real-time measurements of isothermal amplification using turbidity-based measurements," Hashsham said. "But a device doesn't exist anywhere that is able to do real-time isothermal amplification."
With a working protocol in hand, the researchers have now turned their attention to validating Gene-Z in clinical settings to determine sensitivity, specificity, ruggedness, and limit of detection. To that end, they are seeking industrial partners, and have already begun discussions with potential collaborators.