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EraGen Develops SNP Genotyping Software, Expands Capabilities of Compute Cluster

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Along with the news that EraGen Biosciences will provide its single-nucleotide polymorphism detection technology to the Novartis Agricultural Discovery Institute, the company revealed that it has developed new software to speed the SNP detection process.

EraGen CEO Gideon Shapiro said that the company has developed nucleic acid probe design software over the past six months, with a second generation on its way in the next half-year.

EraGen’s technology uses DNA analogs not found in nature, called AEGIS bases (an expanded genetic information system) to construct highly specific recognition codes, known as “era codes.”

These artificial bases form four novel base pairs that don’t recognize nature’s bases, decreasing the number of false positives in SNP detection.

The company has packaged these nucleic acid tags with assays and amplification technologies for SNP genotyping into a product called SNP-Code.

Besides its SNP product, the Alachua, Fla.-based company has developed MasterCatalog, a bioinformatics platform and database of genomic information.

According to Shapiro, EraGen has been able to leverage its algorithm development abilities not only for its genomic databases but also to create the probe software.

The current probe software can be used to design up to 1,000 tags and the second-generation software will be able to design at least 10,000 tags for DNA chip application.

Chris Scherrer, EraGen’s head of probe design software development, led the project that included conducting experiments, determining parameters, measuring data, and then building a model, which has been refined. In the next development cycle, professor Michael Hallett of McGill University will act as a consultant and assist Scherrer.

NADII of La Jolla, Calif., will not have access to the software under the present deal and is not participating in the software development. “We will provide the probes and the assay technology at this point,” said Shapiro. EraGen will provide NADII with the end results and collaborate on the assay development. Terms of the deal were not disclosed.

NADII plans to incorporate EraGen’s technology into a plant genotyping system under development for use in molecular breeding analysis. The system will be used to detect SNP variants in crops that could be associated with higher yields or greater resistance to pests or drought.

“The idea is that we will work together on a system and then in good faith we will work out licensing agreements,” said EraGen CSO James Prudent. “They’re giving us money and we’re developing a technology with that money that we’ll be able to license,” he said.

The company has also licensed this technology to Bayer’s diagnostic unit, which is using it in HIV testing. EraGen’s Era-Code technology can be used to build chip, bead, or any other surface-based genotyping system, said Prudent.

As for the software itself, EraGen is considering whether to make the probe programs available to strategic collaborators that want to make the nucleic acid probes in-house, said Shapiro.

As the development work proceeds on phase two, the second version software will be deployed on EraGen’s bioinformatics compute cluster.

“The same compute infrastructure that we use to make the [genomic] dictionaries will now become very important as we scale up to 10,000 tags,” said Shapiro.

EraGen has invested about $500,000 in its computing infrastructure, which has just been expanded over the last three months.

That system will continue to grow as EraGen intends to double its 100-Intel-processor Linux cluster over the next quarter. A Linux cluster can be built “for roughly a tenth of the price” of a traditional high-performance computing environment, maintained Shapiro.

EraGen has developed software to manage the cluster in a flexible way so that processes can be distributed to enable MasterCatalog databases to be built at the same time as the probe design processes are run. The company relied on its own expertise as well as a subsidiary of the telecommunications company USA Digital to build its cluster.

EraGen has divided its bioinformatics area into three groups: production of the MasterCatalog dictionaries, assay and probe design for its nucleic acid technologies, and a genomic data mining group which uses proprietary tools reserved for internal use.

— Matthew Dougherty and Aaron J. Sender

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