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QuantaLife Unveils Digital PCR Platform; Offers Early Access Before '11 Full Commercial Launch


This story has been updated from a previous version to include pricing information for Fluidigm's digital PCR products.

By Ben Butkus

QuantaLife, a 2008 spinout of Lawrence Livermore National Laboratory, this week unveiled its flagship platform for digital PCR at the American Society of Human Genetics meeting in Washington, DC.

The platform, called the Digital Droplet PCR system, is currently in the hands of early-access users at undisclosed academic institutions, and QuantaLife is making the platform available to other interested parties at an initial cost of $50,000, Mike Lucero, QuantaLife's vice president of marketing, told PCR Insider this week.

However, QuantaLife will not begin full commercial shipment of the new platform until the beta-test period has concluded, likely by the end of this year, Lucero said.

Nevertheless, this week at ASHG QuantaLife is demonstrating the platform and its potential applications, first and foremost copy number variation, which Lucero said is a hot topic at this year's ASHG meeting in the wake of the first publication from the 1000 Genomes Project, an international consortium formed to sequence the genomes of 1,000 anonymous individuals in order to create a comprehensive map of genetic variation, including CNV.

"That's what digital PCR is really good at, which is why I'm introducing the product here," Lucero said.

The Droplet Digital PCR system comprises a droplet generator and a droplet reader, and uses microfluidics and emulsion chemistry to partition each sample, premixed with master mix and primers and probes, into anywhere from 20,000 to millions of 1-nanoliter droplets, each of which contains a separate PCR reaction.

The partitioned samples are then transferred to the wells of a 96-well plate, and the targeted DNA or RNA molecules within each sample are amplified using a standard thermal cycler, according to QuantaLife's website. The droplets within each well are monodisperse.

The droplets are then picked up and streamed single file past a two-color fluorescence detector at the rate of 1,000 per second. The QuantaLife system measures the fluorescence intensity of each droplet to determine the number of PCR negative and positive droplets, according to the company. Unlike real-time PCR, which reports a cycle threshold, the QuantaLife system reports an absolute concentration.

For CNV applications, the system can detect slight differences in gene copy number; for example, six copies from five copies, or a 10 percent difference in mRNA expression, QuantaLife said. The system obviates standardization procedures, as is necessary in qPCR; and can read 48 samples per hour.

QuantaLife has posted on its website an example of a CNV experiment using Droplet Digital, in which 13 samples obtained from the Coriell Institute were analyzed to assess variation in copy number for the gene CCL3L1. The company has also used Droplet Digital to measure the copy number for MRGPX1 from two samples with known copy numbers of four and five. In both cases, the platform was able to distinguish copy number variation with a high degree of accuracy at confidence intervals of 95 percent, the company said.

Beyond CNV applications, QuantaLife will also be promoting applications such as mutation detection. However, CNV will remain the initial sweet spot, Lucero said.

One of Droplet Digital's strongest selling points will be cost, according to Lucero, who said that the platform's price will be about half that of other digital PCR systems on the market, which includes Fluidigm's Digital Array technology, which runs on multiple Fluidigm instrument platforms; and Life Tech's AccessArray digital PCR system, which the company also introduced this week at ASHG (see related story, this issue).

"We are going to quote a price for people who come to the show of $50,000 for the whole system," Lucero said. "People get their $50,000 worth after the first experiment, and then the rest is free."

According to Fluidigm spokesperson Howard High, the price of a full digital PCR setup varies by region of the world and system configuration, but he added that customers can "get into a Fluidigm system for doing digital PCR" for around $100,000.

"If a customer already owns a BioMark System, they can do digital PCR by just buying our Digital Array chips," High added. "The machine will perform real-time or digital PCR."

Life Technologies has not disclosed pricing for its new digital PCR kit or the platform on which it runs, the OpenArray. A request for pricing was not returned in time for this publication.

Both Life Tech and Fluidigm's systems consist of a PCR instrument and physical consumables, the cost of which can drive up the overall price per sample, Lucero said.

"For Fluidigm, the price per sample is tied up in the chip," Lucero said. "I believe it may be 10 times more expensive than our product, because we don't use a chip — we just use oil to create the partitions."

Fluidigm's High told PCR Insider that customers can expect a cost per sample of about $10.