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Biobase Licenses ANNOVAR from USC and CHOP to Add Analysis Software to Variant Databases


Biobase has signed an agreement with the University of Southern California and the Children’s Hospital of Philadelphia that allows it to commercialize Annotate Variation, or ANNOVAR, an open source software tool used for annotating genomic variants.

Biobase said that it will distribute ANNOVAR as a standalone software package that will complement GenomeTrax, a database of diseases, phenotypes, and functional effects of genomic variants that the company has assembled from resources such as the Human Gene Mutation Database.

The free version of ANNOVAR will still be available for academic users.

In addition to purchasing ANNOVAR as a standalone tool, Biobase customers can also buy a bundled product that includes both the software and the GenomeTrax database, Frank Schacherer, the company’s chief technology officer, told BioInform.

Pricing for the software and the bundled product will be determined on a case-by-case basis and by factors such as the number of genomes to be sequenced and analyzed as well as the number of researchers that will have access to the tools, he said.

Biobase decided to license ANNOVAR because a lot of its GenomeTrax customers already use the software in their annotation pipelines and the company decided that if it could make both tools compatible, it could help these clients drill down to relevant results faster, Schacherer said.

“We realized that ANNOVAR is the perfect counterpart to the GenomeTrax database because it allows users to do more sophisticated bioinformatics” than they would be able to do on their own, he said.

Furthermore, Biobase’s “forte” is in providing content and not software development, he continued.

“Our main business is content to help you understand your data,” he said. Therefore, tools that make it easy to leverage genomic information and that are as widely used as ANNOVAR are “good for us,” he said.

Biobase also believes that adding ANNOVAR to its portfolio gives it a competitive edge over other data providers in the marketplace since current and potential customers can get information and tools to make use of it from the same source, he said.

The arrangement benefits USC, which previously sold licenses directly to industry, because “it may attract more sales with the existing customer base and customer support team from Biobase, and significantly reduces administrative burden from university tech transfer offices,” Kai Wang, an assistant professor at USC and one of Annovar’s developers, told BioInform in an email.

The deal with Biobase means that commercial users will now pay the company directly for their licenses instead of USC and CHOP. Wang added that the commercialization step will have no impact on access to the academic version of ANNOVAR, which will remain freely available.

He said the arrangement makes sense because pairing GenomeTrax and ANNOVAR will give commercial users access to more information that could “significantly facilitate their discovery and research.”

It also gives these users a “boost in their ability to mine functional information from genome variants and accelerate biomedical discoveries," he said.

“This is definitely a win-win situation,” Wang said, noting that commercialization is a common move for developers of academic software and technology.

For example, the Broad Institute recently tapped Appistry, a St. Louis-based cloud computing firm, to distribute and support a commercial version of its Genome Analysis Toolkit (BI 10/19/2012).

BioInform was unable to get comment from the technology transfer offices of both institutions about the arrangements with Biobase as of press time.