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Fluidigm Launches Assays and Primers to Reduce Cost of Multiplexed Analysis, Drive Instrument Sales

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By Bernadette Toner

Fluidigm this week launched assays and primers that are expected to reduce the per-assay chemistry costs of large-scale experiments and ultimately drive instrument sales for the company.

The new products — Deltagene assays for gene expression, SNPtype assays for SNP genotyping, and Access Array Target-specific Primers for next-generation sequencing target enrichment — are available in volumes appropriate for Fluidigm's microfluidics technology and are based on flexible chemistries that enable customers to create multiplexed panels using off-the-shelf and custom content.

Fluidigm will provide the assay primer locus sequences with every order, in compliance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments, or MIQE, guidelines.

"From a revenue growth perspective, we expect these consumable products to help enable growth of instrument sales in the near term; and in the medium term allow us to participate significantly in the assays and primers revenue stream … [which] we don't participate in today," said Fluidigm CEO Gajus Worthington during a conference call to discuss the company's first-quarter financial results this week.

"Our goal in getting into chemistries was to further enable our customers to realize the benefits of our microfluidic systems, which enable highly multiplexed analysis," Worthington said. "To reach this goal we needed to address the high cost of label- and probe-based assays. These upfront assay costs can be an impediment to acquisition and utilization of our instruments."

Fluidigm claims that the per-assay costs of its new products are substantially lower than existing probe-based methods such as Taqman assays. Worthington said that the Deltagene assays for gene expression are approximately one-quarter the list price of labeled probe-based methods — approximately $30 instead of $150 — while the SNPtype genotyping assays are about one-seventh the cost of traditional methods — $50 versus $350.

"If your assays cost in the low hundreds of dollars apiece, then looking at 100 at a time or 300 at a time is a really expensive proposition, just in terms of getting started with the experiments," Worthington told PCR Insider in an interview earlier this week.

Over the last few years, he said, "this really emerged as a major problem for our users — that the upfront cost of individual assays really inhibited their ability to run the kind of experiments that they wanted to."

Worthington noted that the pricing problem for its platform was not entirely unexpected. "What we brought to the market was a very high-throughput system that was microfluidic, and nobody had done that before, so nobody had really thought about matching the chemistry to the platform," he said. "The chemistries that were out there were mapped to 384-well plates, not to chips that can do 10,000 reactions at a time where you'd use a tiny, tiny, tiny amount of assay and master mix."

As a result, several years ago the company began searching for chemistries that would suit its needs — namely the ability to maintain a high level of performance while reducing the cost of experiments. "We needed to find the chemistries that really utilized the inherent performance of the system and delivered the data quality that people have become accustomed to, and at the same time reduce costs," he said.

Un Kwon-Casado, director of strategic marketing at Fluidigm, told PCR Insider that the company is using EvaGreen, a next-generation DNA-binding dye, for the gene expression assays; and has developed an allele-specific competitive PCR approach for the genotyping assays.

She added that the company spent "quite a bit" of time "developing a proprietary bioinformatics pipeline and developing a process whereby we wet-test all our assays, so this helps us verify assay specificity, which is very important for our customers."

Kwon-Casado noted that all the Fluidigm systems are open platforms, so customers can still use chemistries from other vendors if they choose to do so.

The Deltagene assays are for use with the company's BioMark HD System and can be custom designed to any reference sequence. The company also offers a catalog of biologically grouped quantitative PCR assays that researchers can customize into panels. Customers receive primers sufficient for more than 100 chips, supplied in a 96-well plate, with a minimum of 48 assays per order. Turnaround time is three weeks for bioinformatically tested assays and six weeks for wet-lab tested assays.

The SNPtype assays run on Fluidigm's EP1 or BioMark HD systems. The company provides primers sufficient for "hundreds" of 96:96 integrated fluidic circuits in a 96-well plate format with a minimum of 24 assays per order. Turnaround time is three to four weeks.

The Access Array Target-specific Primers are available for human and mouse targeted resequencing. Customers receive a 96-well plate containing pooled forward and reverse primers. Fluidigm has not disclosed the turnaround time for the primers.

In addition to the lower costs of the assays, the company expects their compliance with the MIQE standard to be advantageous. In the case of the gene expression assays, Fluidigm provides the primer sequences, a positional map of where all the primers lie, and functional GO ontology information.

"That's the kind of information you can't get if you're not willing to provide sequencing information," Worthington said. "But if you are willing to do that, you can give your customers a lot of information about how the assay is designed, where it lies, and all that is important for the biology."

"We've heard from our customers loud and clear that the release of the primer sequences is really important to them," Kwon-Casado said. "So we think beyond the cost benefit, this is a really strong number two that is really going to differentiate us in the marketplace."

Double-Digit Growth

Fluidigm announced the new assays the day before it reported its financial results for the first quarter, in which revenues rose 30 percent and product sales climbed 34 percent over the prior-year period.

The company also raised its guidance for full-year product revenue growth to a range of between 27 percent and 30 percent. The company had previously forecast an increase of 25 percent to 27 percent.

Fluidigm reported total revenues of $8.7 million for the three-month period ended March 31, compared to $6.7 million for the first quarter of 2010. The company beat analyst estimates of $8.4 million in revenue for the quarter.

Instrument sales rose to $5 million from $4.1 million in the first quarter of 2010, while consumables revenues increased 61 percent to $3.5 million from $2.1 million in the year-ago period, driven primarily by a spike in orders from several ag-bio companies for SNP-genotyping products. Company officials noted that this consumable volume may not be sustainable in future quarters.

Fluidigm's installed base grew to approximately 350 systems during the quarter, comprising 275 instruments that the company categorizes as analytical systems and 75 that it categorizes as sample-prep systems for next-gen sequencing.

The company's net loss for the quarter was $17.2 million, or $1.60 per share, compared to a net loss of $5.6 million, or $3.02 per share, for the first quarter of 2010.

The company's first-quarter R&D spending was flat at around $3.2 million, while SG&A spending increased 21 percent to $7.4 million from $6.1 million.

During the earnings call, Worthington cited single-cell genomics, next-generation sequencing, and ag-bio SNP genotyping as the key growth drivers from the company.

Fluidigm finished the quarter with cash and cash equivalents of $55.8 million and available-for-sale securities of $21.9 million.

Ben Butkus contributed reporting to this article.


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