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QuantaLife to Begin Shipping Digital PCR System in Coming Month


By Ben Butkus

Having successfully beta-tested its digital PCR platform, QuantaLife said this week that it expects to begin commercially shipping the system in the coming month.

In addition, QuantaLife disclosed the identity of one of its beta-test partners, a laboratory at the Fred Hutchinson Cancer Research Center in Seattle that is using the platform for rare mutation detection.

QuantaLife, based in Pleasanton, Calif., said this week that it would be shipping its flagship product, the Droplet Digital PCR System, in July.

The system comprises a droplet generator, which divides each biological sample to be tested into 20,000 1-nL droplets that can then be transferred to well plates and amplified using qPCR; and a droplet reader, where the droplets are streamed past a two-color fluorescence detector that reads each droplet as either positive or negative for the target nucleic acid molecules.

The ddPCR System software then determines the concentration of the selected target in the original sample and provides absolute quantification in digital form.

QuantaLife first unveiled its platform in November at the American Society of Human Genetics meeting in Washington, DC. It said at the time that it was offering beta versions of the system to early-access users and making it available to other interested parties for approximately $50,000 (PCR Insider, 11/4/10).

The company had not disclosed any of its beta-test partners until this week, when Mike Lucero, vice president of marketing at the company, told PCR Insider that the laboratory of Jason Bielas, an assistant member in the molecular diagnostics program at the Hutch, has been working with the platform in recent months.

Bielas told PCR Insider this week that his lab measures rare mutational events with frequencies of as small as one in 109 in nuclear and mitochondrial DNA, and subsequently conducts single-molecule sequencing on recovered mutants.

Until recently, the group was first using endpoint PCR assays and manually diluting mutants according to Poisson statistics; and then using qPCR to increase throughput by putting multiple mutants in single wells and using cloning techniques to recover single molecules.

According to Bielas, however, these approaches have a number of problems. "What you amplify is not always in the correct ratio of what's happening in vivo," he said. "This is because different products have different amplification efficiencies. We were also looking at deletions, and differently sized deletions also amplify at different rates. So what you put into system is not necessarily the snapshot you get out."

"Also, there's the fact that if we're screening millions and billions of copies, and we're only recovering tens or hundreds of mutants, we needed a way in which we could quantify that very accurately," Bielas added. "This is where qPCR kind of falls off, at the very low numbers."

The group had also been preparing to employ emulsion PCR, but also found that technique to be difficult to set up, inconsistent, and not as quantitative as it needed.

"So when QuantaLife came along, [with the ability to] produce 20,000 droplets in a single well, it seemed like the perfect platform for us," Bielas said. "Now that we've used it, it's actually a lot better than we originally thought. PCR seems to be a lot more efficient in the droplets, almost 10-fold more. Typically when we would recover mutants with a number of 10, now we see 100. And the reproducibility among samples is far greater than qPCR, as well."

One drawback to the platform, according to Bielas, is that once the droplets it produces are thermocycled, "they're extremely difficult to break or crack. And once you pass [the droplets] through the detector, you can't recover them." This makes subsequent sequencing of the PCR products challenging.

However, QuantaLife has been working with his lab to address this issue, even though "we might be the only people doing this kind of work," Bielas said. In general, he added, as a beta-tester, the lab continues to work with QuantaLife to "provide what we can in terms of the instrument diagnostic;" and in exchange, QuantaLife has been helping the lab customize specific assays and chemistries to make the ddPCR System more applicable to its research.

Bielas said that his lab has purchased the beta ddPCR System and that QuantaLife will continue to upgrade it as new versions of the platform hit the market.

Have topics you'd like to see covered in PCR Insider? Contact the editor at bbutkus [at] genomeweb [.] com.