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Trovagene Moves to RainDance from Bio-Rad for Digital PCR-based Transrenal Mutation Assays

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Trovagene is using RainDance Technologies' RainDrop Digital PCR system to develop and eventually run a cell-free transrenal BRAF mutation assay out of Trovagene's CLIA lab, the companies said this week.

San Diego-based Trovagene said last week that it had already validated the test, which detects BRAF mutations from cell-free DNA in urine, and said that it would be available sometime this quarter. However, the company did not disclose until this week that it was using the RainDrop system as the detection platform.

PCR Insider reported in November that Trovagene had completed development of a test that would use a different platform, Bio-Rad's QX100 Droplet Digital PCR system, for a different assay that would detect the most prevalent cancer-related KRAS mutations in cell-free nucleic acids from patient urine samples in order to monitor the progression of pancreatic cancer (PCR Insider, 11/29/2013).

Earlier this year, TrovaGene provided an update on its cancer mutation tests, noting that it expected to introduce that KRAS test in the second quarter of this year. It also said in January that it had entered into a collaboration with the University of Texas MD Anderson Cancer Center to detect transrenal BRAF mutations in the urine of patients with advanced or metastatic cancers (PCR Insider, 1/3/2013).

Since that time, however, Trovagene rejiggered its test-development timeline and reconsidered its detection platform, a Trovagene spokesperson told PCR Insider this week.

According to the spokesperson, Trovagene "flip-flopped" the development timelines of the KRAS and BRAF tests, pushing the BRAF test to the forefront due to a more immediate market need based on recently launched therapeutics, and putting the KRAS test on the backburner.

TrovaGene also chose to go with the RainDrop Digital PCR system for its test development. It did so, the spokesperson said, because it yielded a "higher sensitivity for this particular test" and was more amenable to handling the larger-volume urine samples that are required for the transrenal assay.

The spokesperson added that the switch to the RainDrop platform from the QX100 was "not an all-or-nothing" event, and that Trovagene is still conducting research with the QX100. She also noted that the KRAS test was still under development, but couldn't confirm whether Trovagene was also looking to switch this assay to the RainDrop system. However, she pointed out that the same characteristics of the system that makes it ideal for the BRAF assay would apply to the KRAS assay.

RainDance launched the RainDrop platform under an early-access program in March 2012, thus challenging the only other droplet-based system on the market at that time, the QX100.

In a statement, RainDance said that the RainDrop System enables a hundred-fold increase in the amount of DNA that can be analyzed for cancer mutation detection, thereby increasing sensitivity and the ability to find rare mutations. The platform can analyze up to 10 million picoliter-sized droplets in a single assay, vastly improving the probability that low-level mutations will be detected. The system also enables quantification of the relative amounts of mutated DNA in a sample, according to the company.

"Trovagene's goal is to help improve detection and monitoring of cancer patients undergoing treatment, particularly those with metastatic cancers," Trovagene CSO Mark Erlander said in a statement.

"Analyzing the large amounts of DNA present in urine requires a platform capable of handling hundreds of thousands, if not millions, of reactions," he added. "The high level of sensitivity and workflow improvements made [RainDrop] a clear, cost-effective choice for detecting and quantifying singular oncogene mutations from cell-free DNA."

Other users are starting to weigh in on the RainDrop's benefits from both a research and clinical diagnostics perspective. For instance, last week researchers from Massachusetts General Hospital published a method using the RainDrop system to detect mutations associated with glioblastoma brain tumors in tumor-derived RNA extracted from extracellular vesicles in patients' cerebrospinal fluid (see related story, this issue). That group indicated that it would also be evaluating Bio-Rad's platform for its assay.

Also this week, Bio-Rad launched a new version of its digital PCR platform, the QX200, which incorporates the ability to work with EvaGreen intercalating dye chemistry (see related story, this issue).

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