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Trovagene Using Bio-Rad Digital PCR System for Trans-Renal Pancreatic Cancer MDx

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This article has been updated from a previous version to correct the list price of the QX100 system.

A Trovagene official this week disclosed that the company is using Bio-Rad's QX100 Droplet Digital PCR system for a non-invasive, urine-based molecular test it is developing to detect and monitor the progression of pancreatic cancer.

Antonius Schuh, Trovagene's CEO, also said that the company has validated the test in house and will soon begin clinical trials for it. The test is designed to detect the most prevalent cancer-related KRAS mutations in cell-free nucleic acids from patient urine samples.

If the clinical trials are successful, Trovagene will offer the assay on the research-use-only QX100 as a laboratory-developed test out of its San Diego-based CLIA-certified laboratory, recently acquired from MultiGen Diagnostics.

Schuh discussed Trovagene's development work on the QX100 platform this week as the company kicked off a public offering intended to bring in gross proceeds of $9.2 million. Trovagene currently trades as an over-the-counter stock and the new offering, combined with a one-for-six reverse stock split, will allow it to transfer its shares to the Nasdaq. The offering is expected to close on June 4.

"From the early experience that we have with the [QX100], we are very happy with it," Schuh told PCR Insider. "It seems robust and highly reproducible. It works beautifully."

Earlier this month, Trovagene disclosed that it had successfully completed the analytical development of digital PCR assays to detect KRAS mutations in cell-free nucleic acids from patient urine samples with the end goal of commercializing a test that could help doctors non-invasively diagnose and monitor pancreatic cancer progression (PCR Insider, 5/3/2012).

Schuh noted at the time that, in general, the company had chosen digital PCR as its development platform due to its ability to detect low-level mutations in large amounts of wild-type background, and said that Trovagene had decided to use a specific commercial digital PCR platform, although he declined to say which one.

This week, Schuh identified the platform as the QX100 and outlined Trovagene's rationale for choosing that system.

"First of all, the system is very cost-competitive … and the operating cost, the cost of reagents and materials, is also lower," he said. "That is, of course, a big plus."

The QX100, which sells for approximately $89,000, comprises a droplet generator that divides each biological sample to be tested into 20,000 1-nL droplets in conventional PCR well plates. The samples are then amplified in the plates on a standard thermal cycler, and the plates are subsequently placed in a separate droplet reader, which features a two-color fluorescence detector that reads each droplet as either positive or negative for target nucleic acid molecules.

Bio-Rad acquired the QX100 along with its original developer, QuantaLife, in October in a deal worth approximately $162 million (PCR Insider, 10/6/2011).

"We liked very much that the system seamlessly integrates [with our] established PCR setup," Schuh said. "Essentially, you do what you did before – you extract your DNA, purify your DNA, and make your PCR setups in a conventional microtiter plate – and then all you do … is convert that sample into [droplets] … before you insert that microplate in your conventional thermal cycler."

These steps take place in a laboratory's dedicated preparation area, "so you can maintain the physical separations required to minimize contamination risk," Schuh said. "You can maintain all that, and once you have cycled your [droplet] microtiter plate, instead of using a plate reader … you then insert that plate into the second component for the readout. The change of workflow is minimal, and you maintain the standard arrangement in your lab, and at a price that is very competitive."

Neither Bio-Rad not predecessor QuantaLife has spoken much publicly about the clinical potential of the QX100. The company was unable to provide comment prior to publication of this article. However, in 2010 QuantaLife was awarded a five-year grant from the National Institutes of Health to explore the use of its platform to detect methicillin-resistant Staphylococcus aureus for prevention and surveillance purposes (PCR Insider, 8/26/2010).

The platform is currently for research use only, but Schuh noted that Trovagene would be able to offer its assay as a LDT so long as it validates the system within an analytical setup for use within a CLIA lab.

"This would be a conventional LDT system, and we follow the same procedure [as] everyone who uses, let's say, a Sanger sequencer in a lab — that's a RUO instrument, and it has to be validated for your purpose," Schuh said. "Under the CLIA regulations, we can use … reagent and instrument components that are considered research use only for specific applications, provided that we validate them for that application."

Trovagene in February closed the acquisition of the CLIA laboratory of MultiGen Diagnostics, the molecular diagnostics subsidiary of Bio-ID Diagnostics. The lab is certified by the State of California in compliance with CLIA and is accredited by the College of American Pathologists.

Trovagene has previously published research by the company and its scientific collaborators that demonstrated that KRAS mutations — which have been implicated in more than 90 percent of pancreatic cancers and in 23 percent of solid tumors — can be more reliably detected in urine as compared to plasma or biopsy material.

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