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Researcher Wins SBIR Grant to Develop 'Universal' PCR Probe Library; Seeks Commercialization Partners

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By Ben Butkus

An independent researcher from the Pacific Northwest has been awarded a Phase I Small Business Innovation Research grant from the National Institutes of Health to establish a so-called "true universal library" of extremely short fluorescence-based PCR probes.

In addition, the researcher, Igor Kutyavin, has founded a nucleic acid chemistry, detection, and amplification consulting firm called Perpetual Genomics as a vehicle to license the technology and related intellectual property to larger partners to further develop and market the technology and universal probe library.

If developed into a commercial offering, the probes could have "a huge economic effect" by reducing the amount of probes typically wasted in real-time PCR experiments, slashing the cost of probes by approximately 10-fold, and significantly increasing the throughput of genomics research, Kutyavin told PCR Insider this week.

The Phase I SBIR grant, awarded by the National Institute of General Medical Sciences at the beginning of June and worth a little more than $100,000 over six months, is meant to support the development of a PCR system that would use extremely short (6-mer to 8-mer or less) Förster resonance energy transfer, or FRET, probes for nucleic acid detection in post-PCR and real-time PCR, according to the grant's abstract.

The eventual goal of the grant is to enable the development of a universal probe library that would allow fractional sale of such FRET-based probes. Each probe would cost almost the same as primers, Kutyavin said, meaning as little as $10 to $15 a probe – about one-tenth that of typical PCR probes such as TaqMan, which at their most inexpensive cost in the neighborhood of $150 per probe.

"I'm not going to improve the signal or detection or quality of quantitative real-time PCR," Kutyavin said "My goal is to maintain the same efficiency of probe-based real-time PCR … and allow the sale of probes fractionally."

Kutyavin explained that researchers usually need just 1 percent of the amount of a probe they receive from manufactures, while the remaining portion is usually wasted. "If manufacturers could sell that 1 percent of the probe amount, the cost of the probes for the majority of users will drop by an order of magnitude," saving both manufacturers and customers money "and accelerat[ing] genomic research significantly," he added.

Another key feature of the universal probe library would be that it would contain a complementary probe component for any given target DNA sequence for any potential application or organism.

"A universal library is supposed to cover everything, every possible application," Kutyavin said. "This means multiplexing, SNP detection, microRNA … and any sequence in the world – plants, humans, bacteria. You don't need to specify, you just have a universal library."

Other tool vendors have attempted to develop a universal probe library, most notably Roche, which has a license to Exiqon's locked nucleic acid technology to develop the probes. Roche's UPL comprises 165 short hydrolysis probes incorporating the LNA technology to detect 8- and 9-mer motifs in the human transcriptome. This offering, according to Kutyavin, is not truly universal because it only applies to gene expression profiling and cannot be applied to SNP or microRNA detection, and detects only relatively GC-rich regions.

"I want to make this absolutely sequence-independent, and the probes should be much shorter," Kutyavin said. According to Kutyavin, if he can create a universal library of 6-mer probes, the library would contain 4,096 members; and for 4-mer probes, this number would drop to a 256-probe library. Assuming the Phase I portion of the SBIR grant is successful, Kutyavin's eventual goal is to create a universal library of 4-mer probes

"I've already got a good signal on the 4-mers, but this consisted of three GC base pairs along with one AT," Kutyavin said. "I have to show that AT-rich targets would work as well. But I'm very confident that I am down to 6-mer. The shorter you go without sacrificing performance, it becomes more economical, and more attractive and economical for the manufacturer and scientists."

To try and market his idea, Kutyavin has created Perpetual Genomics, a company for which he is the founder, CEO, and sole employee. In the short term he hopes to draw on his experience in nucleic acid chemistry – he was one of the original developers of major groove binder technology, now used in Life Technologies' Applied Biosystems TaqMan probes – to generate revenues.

However, in the long term, as he validates his technology using SBIR funding, Kutyavin hopes to find a commercial partner.

"Eventually I am looking to sell a license to this, and I am looking for someone who can bring this to market," he said.

In the meantime, after having applied for a provisional patent on his concept and technology "a while ago," Kutyavin is currently working with his lawyer to apply for the additional patents necessary to present a licensable package to potential partners, he said.

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