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Appistry to Commercialize Broad Institute's Genome Analysis Toolkit

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The Broad Institute has tapped St. Louis-based cloud computing firm Appistry to distribute and support a commercial version of its Genome Analysis Toolkit.

The agreement permits Appistry to make GATK available to users at for-profit companies under a license that will cover commercial-grade support for installation, configuration, and documentation.

Trevor Heritage, Appistry’s vice president of marketing and sales, told BioInform that for-profit groups can begin purchasing licenses to GATK 2.0 as early as this week for an undisclosed annual subscription fee that will be determined by the size of the customer in question and the number of users at each site.

Academic users will continue to have free access to GATK through the Broad Institute's website.

Appistry has historically catered to the defense and financial markets but threw its hat into the bioinformatics ring last year with the launch of Ayrris/Bio, a dedicated cloud offering for the genomics market (BI 9/9/2011).

The Broad agreement is a potentially profitable one for Appistry as it now has access to a much larger pool of customers from the GATK user community. The partnership opens the door for “[us] to talk to … [those] customers about their pipelines and about their throughput needs” as well as “about how we might help them scale that pipeline that they have built to their needs,” Heritage said.

Although GATK offers some of the same capabilities as Ayrris/Bio, Appistry doesn’t see it as a competing product because its business focus isn’t selling bioinformatics applications, CEO Kevin Haar said.

Rather, analysis pipelines like GATK provide a foundation from which Appistry can help customers build broader cloud-based infrastructures, Haar explained.

“We are much more focused on accelerating the science for our customers and accelerating the approach that they want to take” using “whatever combination of the dozens of bioinformatics tools that they may have or they may want to leverage into their own personal pipeline,” he said.

Appistry's current bioinformatics clients include the University of Missouri; Stanford University School of Medicine; the University of California, Davis; the Children’s Hospital of Philadelphia; and the Emory Winship Cancer Institute (BI 1/30/2012).

Commercializing GATK

In selecting a commercialization partner for GATK, the Broad sought a vendor who could offer “higher levels of support” than the institute’s limited resources can sustain, as well as provide resources to further develop the toolkit, David Altshuler, deputy director of the Broad Institute, told BioInform.

It was also “critical to us that any partner be supportive of the ongoing open source nature of the framework and that we would be able to give the tools to any academic, not-for-profit research user without any restriction or cost,” he said. “We met with a number of companies and Appistry proved the best fit.”

Earlier this year, Mark DePristo, who leads the genome sequencing and analysis group in the Broad’s Medical and Population Genetics program, told BioInform that the institute was mulling a commercial licensing scheme for GATK because of requests from for-profit groups for greater support than the developers had the resources to provide.

In addition to receiving greater support, DePristo said the Broad also hoped to address the needs of users in restricted environments, such as CLIA-certified laboratories, who couldn’t keep up with the GATK’s release cycle and whose versions of the toolkit were no longer supported (BI 8/3/2012).

Under its arrangement with the Broad, Appistry will support several GATK releases per year but not all of them, Heritage said.

“Our plan is basically to have several releases a year and when we package up a release, what we will be doing is providing commercial quality assurance on that as well as bringing together whatever the latest and greatest set of feature functions is that the Broad has developed in their interim period,” he explained

Financial details of the arrangement between the Broad and Appistry aren’t being disclosed but Heritage told BioInform that the partners have a “typical” royalty-based agreement “that compensates [Appistry] for the go-to-market deliverable and provides [the Broad] the remainder of the funding to be used for R&D.”

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