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Fluidigm, Qiagen's SABiosciences Optimize PCR-Based Gene Expression Panels for Microfluidics Platform

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By Ben Butkus

Fluidigm and SABiosciences, a Qiagen subsidiary, have partnered to offer more than 100 pathway-focused gene expression panels validated for real-time PCR analysis on Fluidigm's BioMark system, Fluidigm said today.

The alliance marks the first time Fluidigm has worked directly with another vendor to optimize gene-expression assays specifically for the microfluidics-based platform, and is expected to provide users with a source of validated pre-defined or custom gene expression panels to use in their research, company representatives said.

For SABiosciences, the deal is expected to generate new customers such as pharmaceutical and biotech researchers that necessitate the higher level of throughput offered by the Biomark platform, company officials said.

Under the agreement, SABiosciences has developed and will continue to develop its PCR-based assay panels, called PCR Arrays, for use on Fluidigm's Dynamic Array chips, which use the company's integrated fluidic circuit technology and are processed and analyzed on the BioMark instrument.

Once Fluidigm has tested the optimized panels in house, sales teams from both organizations will market the assays as complete kits called RT Profiler PCR Arrays, the company said.

Each reagent kit includes pre-aliquoted reagents and primers needed to synthesize first-strand cDNA for subsequent pre-amplification and pathway analysis, and contains enough reagent for five 96.96 Dynamic Array chips, Fluidigm said. The arrays will come in 96-well format, which will allow researchers to quickly set up assays on either the 96.96 or 48.48 chips, the company said.

SABiosciences' real-time PCR Arrays include gene-specific qPCR assays for a set of 96 genes relevant to a pathway or disease state as well as several quality-control elements — a housekeeping gene panel to normalize the data, a genomic DNA control primer set to detect non-transcribed genomic DNA contamination, reverse transcription controls, and positive PCR controls to test the efficiency of the PCR reaction.

The arrays have also been optimized for RNA prepared from fresh and frozen cells and tissues; small samples, and formalin-fixed paraffin-embedded samples, according to SABiosciences.

Lisa Isailovic, a product manager for Fluidigm's gene expression products, told PCR Insider today that the agreement is in line with Fluidigm's desire to make BioMark an open platform.

"This is the first set of panels we have received from a vendor for testing," Isailovic said. "People using the BioMark platform can now call SABiosciences up for pre-defined assay panels including 96 different genes; or they can request a customized panel."

Isailovic added that BioMark customers can use gene-expression panels and kits from a number of other vendors on its system, but they don't come with the guarantee that they are optimized for use on the Dynamic Array chips, which are capable of producing 9,216 real-time qPCR data points in the same amount of time as a single 384-well plate, while using 200-fold less reagent, according to the company.

"The more complete platform we can offer to our customers, the better," Fluidigm spokesperson Howard High told PCR Insider. "Researchers know that by adopting the Fluidigm platform, they get a great workflow and cost and time savings," he added. However, they do not always have the time or expertise to design gene expression panels that maximize the throughput that the company's microfluidics-based workflow offers, he said.

Isailovic said that reducing the amount of reagent used in the PCR Arrays was a big part of optimizing them for BioMark, but SABiosciences also made some changes to the workflow that Fluidigm needed to test out.

In addition, according to Jeff Hung, senior director of marketing at SABiosciences, a key component to the optimization process was incorporating a pre-amplification step to generate a detectable amount of mRNA from the minute amount present in samples being loaded on the Dynamic Array chips.

Sales teams from both companies will offer the optimized kits, High said. Isailovic added that it was too early to tell whether Fluidigm would be able to leverage SABiosciences parent Qiagen's worldwide sales force, but that talks have already begun about how Qiagen's distribution network might factor into the partnership.

And, High added, "As we go forward, we expect that we'll see more of SABiosciences' offering optimized for Fluidigm's platform," although he didn't elaborate.

On SABiosciences' front, the BioMark system joins a relatively comprehensive list of instrumentation systems for which the PCR Arrays have been optimized. According to SABioscience's website, these include RT-PCR platforms from Life Technologies' Applied Biosystems group; Bio-Rad; Eppendorf; Roche; Agilent's Stratagene unit; and Takara. In addition, the assays will soon be optimized for use with Qiagen's Rotor-Gene Q, the company said.

Qiagen acquired Frederick, Md.-based SABiosciences in December for $90 million, primarily for the PCR Arrays product line. The company said at the time that the arrays might help Qiagen and its pharma partners develop companion diagnostics by leveraging technology from another recent Qiagen acquisition, DxS (see PCR Insider 11/17/2009 and GenomeWeb Daily News 9/23/09).

Currently, the majority of SABiosciences' PCR Array customers are in academia – Qiagen said that its new subsidiary was expected to generate around $24 million in revenues this year.

But the partnership with Fluidigm is also expected to open up new markets for SABiosciences in the form researchers who are using a BioMark platform to increase throughput and minimize reagent expenditure.

"The customer base of Fluidigm will be different from many of our current customers in that they will be analyzing many more samples simultaneously," Shankar Sellappan, SABiosciences' PCR Array product manager, told PCR Insider. Those customers are primarily located at pharma and biotech companies and core labs, or are conducting specialized research such as stem cell research, he added.

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