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Life Tech Begins Selling First Digital PCR Product for OpenArray Platform

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By Ben Butkus

Life Technologies this week announced the availability of a kit to perform digital PCR applications such as rare allele detection and absolute quantitation on the OpenArray real-time qPCR system, marking the company's first commercial offering in the dPCR space.

The platform will immediately compete with Fluidigm's Digital Array technology, heretofore the sole dPCR product on the market; as well as with QuantaLife's Droplet Digital system, which was also unveiled this week but won't be fully commercially available until 2011 (see related story, this issue).

Life Tech launched its platform this week in a presentation at the American Society of Human Genetics meeting in Washington, DC. The new system combines "foundational" intellectual property assumed by Life Tech after its acquisition last year of microfluidics firm Cytonix with the OpenArray PCR platform, which Life Tech gained when it acquired BioTrove, also in 2009.

In a July interview with PCR Insider, Gordon Janaway, product manager for real-time PCR reagents at Life Tech, said that the company had been working with BioTrove even before the acquisition to integrate OpenArray – the defining feature of which is an array of 3,072 nanoliter-scale "through-holes" – with TaqMan-based PCR (PCR Insider, 7/8/10).

Since that time, Life Tech has been offering a medium-density solution for PCR-based SNP analysis of hundreds of thousands of samples, but Janaway had said at the time that the company was gearing up to enter the dPCR market with its first product based on OpenArray by the end of the year, and had already begun beta-testing the product with undisclosed users.

This week the company made good on its promise with the launch of its new OpenArray dPCR kit.

"It is a complete solution including reagents, the OpenArray consumable, and software," Janaway told PCR Insider this week. "It works on existing OpenArray real-time PCR systems." Janaway added that existing OpenArray customers "don't need to upgrade their system or change anything. The software fits with their existing software."

Janaway said that one important technological aspect of the new product addresses dPCR's inherent narrow dynamic range.

"Customers that are used to seven or eight logs of dynamic range with qPCR will find that with digital, if their sample is too concentrated, every well will light up positive; and if it's too dilute, every well will be negative, so it's important to find that sweet spot for dPCR."

Life Tech addressed this issue by designing the system to allow users to "place as many serial dilutions as possible in their digital array, so that by introducing several dilutions across their target range, then they will have some that are above the concentration, some below, and some in that sweet spot," Janaway added.

"It's a way to make a much easier workflow for dPCR," he said. "So if you have that serial dilution, then that extends the dynamic range, which means it's easier to get an answer."

Janaway said that the OpenArray software takes any serial dilutions into account and incorporates those into the dPCR analysis.

In fact, much of the new dPCR offering's capabilities are driven by the software that Life Tech developed. For instance, "with digital PCR you can perform the partitioning, and then you can perform PCR and just see the result of PCR positive or PCR negative," Janaway said.

"We chose to do more than that," he added. "We chose to collect real-time amplification curves for each well. That means, in a dilution series, if you're a little too concentrated, you can still see that you have one or two copies present in a well. It's a way of providing more information." Real-time amplification curves also allow users to better control the quality of their results by excluding outliers, Janaway said.

As far as consumables go, the OpenArray consumable will be an "inflexible, hard form factor" designed to greatly reduce volume variation across reaction wells.

"We spent some time characterizing and selecting the consumables for digital PCR so that we have less than 10 percent variation in replicate volume across the plate," Janaway said. "That ensures you have uniformity in the volume, which translates into reproducible and precise digital results."

This is different from Fluidigm's digital PCR chip, which has an "elastomeric, or soft, form factor," Janaway said; and is in stark contrast to other digital PCR products nearing market, such as QuantaLife's Droplet Digital, which uses emulsification to generate uniform individual nanoliter reaction volume droplets.

"I'm not saying those aren't uniform," Janaway said. "But we chose to have this rigid format, and spent a lot of effort characterizing and QC'ing our OpenArray consumable so it will have very low volume variation."

Life Tech will initially market its new platform heavily toward users wishing to explore rare allele detection and absolute quantitation; though Janaway said the company has compelling data for copy number variation applications, as well.

"One of the key applications for dPCR is in rare allele detection," he said. "That's got a couple of components. One of them is designing your system to pick up a single molecule, which every digital platform needs to do, and ours does. Another one is making sure that you interrogate a reasonable sample volume. Our system will interrogate up to about 150 µL of the customer's sample. It can range from 1 µL up to 150 µL."

This would allow users to, for example, count HIV particles in plasma "where there is a very low number of virus particles in the plasma," Janaway said. "Then if you expect only a few copies per 100 µL, you can pick that up with this."

Life Tech this week also identified a pair of beta-testers for the dPCR product: Mikael Kubista, CEO and founder of TATAA Biocenter; and Sui Huang, a professor conducting stem cell research at the University of Calgary.

"The precision of the digital PCR approach is very high, which presents an advantage for several applications such as copy number variation studies — particularly when it is critical to prove a small difference," Kubista said in a statement.

"With conventional qPCR, it is difficult to distinguish samples with two or three copies," Kubista added. "But with digital PCR, one can readily distinguish between four and five copies, and sensitivity can be pushed even further using larger arrays."

Also in a statement, Huang said that when using traditional qPCR, "the measurement you acquire is relative to a reference gene. But with digital PCR, one can reach an absolute measurement of a gene of interest — although you will need 250 to 500 parallel reactions. Some systems biology applications require such measurements; thus, we found that the OpenArray technology is perfect for this type of study."

Janaway said that although the company expects existing OpenArray users to benefit from the new kit, it will also afford an opportunity to sell more platforms to new customers looking for a ready-made solution for dPCR. Life Tech did not disclose a price for the OpenArray platform or the new software and consumable.

Life Tech will also be demonstrating the new dPCR product at the upcoming Association of Molecular Pathologists meeting in San Jose.

"I mentioned quantifying HIV; and at another presentation [at ASHG] we are showing some results on quantifying BK virus," Janaway said. "I think as we've talked more with early-access customers, viral quantitation or pathogen quantitation is a really interesting area for digital PCR. We're going to be exploring that more at AMP and in our ongoing marketing efforts."

Janaway said that Life Tech will officially be taking orders for the new product this week at ASHG and will officially begin shipping product next week.

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