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Asuragen Launches Cancer Panels Optimized for FFPE Tissue; Plans to Sell Proprietary Reagents

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Asuragen has launched two next-gen sequencing cancer panels and plans to roll them out as services in its CLIA-certified laboratory by the beginning of June. The panels, SuraSeq-200 and SuraSeq-500, assess 200 and 500 hotspot mutations across five and 17 oncogenes, respectively.

The panels were designed in-house using proprietary reagents and methods and have been optimized to assess samples from low-quality formalin-fixed, paraffin-embedded tissue. Asuragen eventually plans to market the reagents themselves as products.

The most recent panels complement the company's other offerings — a 52-gene panel that runs on Illumina's Genome Analyzer; a 16-gene panel and a 5-gene panel, both of which were launched on Life Tech's Ion Torrent PGM; and Life Tech's Ion AmpliSeq Cancer panel, which analyzes hotspot mutations in around 46 genes. Asuragen launched these panels last year, as its first products in the next-gen sequencing space (CSN 1/4/2012). These panels are offered for research only.

SuraSeq-200 and SuraSeq-500 are platform agnostic and can run on Ion Torrent or Illumina sequencing platforms, CEO Rollie Carlson told Clinical Sequencing News.

The company currently has an Illumina Genome Analyzer, an Illumina MiSeq, and an Ion Torrent PGM in-house, as well as RainDance's RDT 1000 system and Fluidigm's Access Array for enrichment.

Asuragen designed the panels in-house using its own proprietary reagents, as opposed to those sold by Illumina or Life. As such, the panels have been optimized specifically for formalin-fixed, paraffin-embedded tissue, Carlson said.

Gary Latham, director of diagnostic research and technology development, further explained that the company's proprietary reagents were designed to "accommodate degradation associated with FFPE DNA." Additionally, company researchers developed new bioinformatics to take into account the additional noise caused by FFPE.

"There aren't good tools for calling low abundance variants from FFPE samples," Latham said. The degradation and crosslinking inherent in FFPE create noise, yet the bioinformatics have to get beyond that noise and still be able to call rare variants.

In a validation study of its SuraSeq assays, published in the Journal of Molecular Diagnostics earlier this year, Assuragen researchers found that the background noise from FFPE samples was two-fold higher than that from cell-line DNA, and they were able to adjust their bioinformatics algorithms accordingly.

Another key to the panels is the company's two-step PCR procedure, which generated amplicons between 61 bases and 80 bases. Keeping the amplicons short "minimizes the amplification burden of FFPE DNA templates," the authors wrote in the study.

Because the panels have been designed specifically for FFPE samples, Latham said that they can produce results even from very low-quality samples that would not be able to be sequenced with kits from Life or Illumina.

For instance, said Carlson, when Asuragen tested over 500 FFPE samples that it received from its pharmaceutical collaborators, only between 20 percent and 60 percent of the samples could be assessed with panels designed by the various sequencing vendors, while 80 percent of the samples could be assessed with Asuragen's panels.

Latham said that one reason for the discrepancy is that the vendor-designed panels are often created using only "high-quality FFPE samples," which are not representative of what is frequently seen in clinical settings and from pharmaceutical companies.

The company also plans to use its multiple next-gen platforms, as opposed to Sanger sequencing, for confirmation.. In the validation study, it found that both the Illumina GA and the PGM were better at detecting low-level mutations than Sanger sequencing.

Asuragen tested the three platforms across 38 FFPE colorectal cancer samples, identifying 29 mutations, five of which were undetectable by Sanger sequencing because they were present at frequencies below Sanger's limit of detection.

Latham said that as a result, the company now plans to do confirmation with orthogonal next-gen platforms. So, if it runs a panel on an Illumina platform, it will confirm with the PGM, and vice versa.

"If you reflex to Sanger, you will miss things," he said. "But, by using the two NGS platforms together, we're able to capture those lower frequency mutations."

The company plans to begin offering the SuraSeq panels as a service in its CLIA-certified laboratory by the beginning of June. It is also planning to eventually sell its reagent kits as products. "Assuming the performance we see in the clinical environment, they will be made available to others," Carlson said. "I anticipate that will happen within the next six to 12 months."

Latham added that the company has not yet decided how it will market its reagents, whether as research-use, as a laboratory-developed test, or whether it will take them through US Food and Drug Administration clearance.

While the company has to compete with others that offer next-gen sequencing panels, including Foundation Medicine, which offers a much larger panel that encompasses 236 genes, Latham said that what sets Asuragen apart is its focus on developing panels that can accommodate low-quality samples, which are most often found in clinical settings.

"There are very grave limitations on the availability of material," he said. "We create a lot of high-value mileage with low samples [that] target the regions of most interest to pharma."

There are "diminishing returns as the panels get larger and larger," he said. Sample input requirements are higher, interpretation becomes more difficult, and turnaround time and cost increase, he said.

Latham added, however, that Asuragen plans to add more panels to its mix, some of which may be larger, but that it would remain focused on targeted sequencing.

"We foresee that targeted sequencing will remain an important area that will continue to gain traction in the diagnostic space," he said.

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