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Fluidigm and Roche 454 Co-Promoting Amplicon Sample Prep, Next-Gen Sequencing Platforms

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By Ben Butkus

Fluidigm and Roche's 454 Life Sciences have inked a worldwide co-promotional agreement that combines the companies' amplicon sample prep and high-throughput sequencing platforms to enable inexpensive and highly targeted sequencing, the companies said this week.

Under the terms of the agreement, sales and marketing staff from both companies will trumpet the benefits of using Fluidigm's Access Array system to process 48 samples against 48 amplicons to yield PCR products that are ready for emulsion PCR amplification and sequencing on 454's GS Junior or GS FLX system.

According to the companies, the partnership offers users a "robust and streamlined" workflow that minimizes the number of manual steps required for targeted sequencing applications, including genotyping and rare variant detection.

Access Array is "a sample prep platform that, when used with a [454] system, really enables a whole new set of applications on the sequencer itself," Martin Pieprzyk, a product marketing manager for Fluidigm, told PCR Insider this week.

The companies said that as sequencing PCR products has become more critical for analyzing disease-associated genes in oncology, immunology, and virology, sequencing systems such as those offered by 454 enable rapid comprehensive analysis of large numbers of samples. However, they have also shifted the workflow bottleneck to amplicon sample preparation, a process that can take weeks using traditional methods.

As an example, combining Access Array with 454's GS Junior sequencer will enable researchers to "sequence 48 samples and 48 amplicons at the same time, with maybe 20 minutes of hands-on time in terms of sample preparation," said Pieprzyk. "If you didn't have that combination, you might be able to do four or five samples; it might take you two or three days; and the data quality would not be nearly as high as it is with the Access Array system."

The upshot, added Pieprzyk, is that by adding Access Array to the front end, 454 is "literally taking their existing instrument and transforming it into something entirely new and enabling, and very much competitive with anything else on the market in terms of targeted resequencing. Both companies see the synergies between the systems, and that one system alone is not nearly as powerful as a combination of the two."

In a statement, 454 President and CEO Christopher McLeod said that the combined platforms "allow analysis of large numbers of sample/amplicon combinations in an affordable workflow, without the need for complicated liquid handling. In essence, a single Access Array plate on a single GS Junior system run generates as much data as hundreds, even thousands, of 96-well plates analyzed on a capillary sequencing system."

The companies have no financial agreement in place, meaning that each firm is still selling its instruments independently. However, Pieprzyk said that Fluidigm and 454 "are doing cross-training on both sales teams; we are releasing co-marketing materials like data sheets and product literature; we're setting up a dedicated website for the two systems together; and we'll be presenting data at various conferences on the combined systems."

In addition, each company will make sure to revisit its current installed customer base to explain the benefits of using the combined platforms.

"Clearly we'll be out seeking new opportunities on both our front and on 454's front, and cross selling," Fluidigm spokesperson Howard High said. "But if we have a customer for Access Array right now, and we know they are interested or active in the targeted resequencing area, we're going to make sure they understand the benefits of this combination, and 454 will be doing the same."

Fludigm's Access Array can be used for sample prep applications on several other next-generation sequencing platforms, including the Illumina Genome Analyzer II and Life Technologies SOLiD 4. However, 454 is the first company to work with Fluidigm to promote the use of Access Array with its sequencing platform, Pieprzyk said.

"The same chemistry approach and the same system can be used for SOLiD, Illumina, Pacific [Biosciences], or Ion Torrent; and all the same benefits do apply," he said. "It's simply that at this point for 454, due to their longer read lengths, it's the best approach. But the same approach works for all current sequencers on the market."