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Interactive Biosoftware Adds High-Throughput Variant Annotation Software to Portfolio

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By Uduak Grace Thomas

Interactive Biosoftware has released a new version of its flagship Alamut mutation analysis software designed to identify variants in next-generation sequence data.

Prior to its launch last week, the tool, dubbed Alamut High-Throughput, was tested by clinical laboratories in the US and Europe, including the Partners Healthcare Center for Personalized Genetic Medicine; the Dutch Academic Medical Center; and the Institute of Genetics and Molecular and Cellular Biology in Strasbourg, France.

Partners Healthcare evaluated the product as one of several variant-annotation methods it is considering as part of its effort to launch a whole-genome sequencing service later this year, Matthew Lebo, assistant laboratory director for PCPGM's molecular medicine lab, told BioInform this week.

Interactive Biosoftware's new release is a companion to Alamut, which is targeted for the medical genetics market and serves as a data-integration and -visualization tool to help users interpret specific mutations within the context of the genome (BI 3/4/2011).

Andre Blavier, Interactive's founder and CEO, explained to BioInform this week that Alamut HT incorporates some of the same capabilities of its predecessor, but is intended for use in analysis pipelines to detect variants in whole-genome and whole-exome sequence data rather than as a front-end tool for inspecting mutations.

Alamut HT is better suited for users looking to annotate large number of variants and it doesn't include the visualization capabilities that are available to Alamut users, he said.

Alamut HT is currently available as a cloud-based client-server system for $2,000 per year for a single instance, or as a standalone installation that includes an automatically updatable database for $5,000 per year per instance.

Blavier told BioInform that beta testers have praised the "comprehensiveness" of Alamut HT's annotations, which include information on the effects of variants on human genes, information on SNPs, and missense and splicing predictions.

Alamut and Alamut HT both incorporate five splicing-prediction algorithms in addition to PolyPhen and SIFT, Blavier explained to BioInform.

"As far as we know, no other current annotation tool provides [splicing prediction tools], he said.

PCPGM's Lebo's impressions of Interactive's new software were that "it does what it says."

Alamut HT "has a pretty rich database of variant annotation and it is able to get us the data in a format that we are then able to apply our own algorithms on," he told BioInform.

It also saves his lab's small bioinformatics staff the trouble of developing a similar platform in house, although it has not ruled that option out, he said.

PCPGM is developing a method of screening for genetic variants associated with conditions like cardiomyopathy, hearing loss, and cancers, among other ailments.

'Not a Services Company'

Rouen, France-based Interactive Biosoftware is "doing very well" in European markets and its business is growing in North America with about 30 customers on that side of the hemisphere using its software, Blavier said.

However, the company of five intends to step up its activities in the US and Canada and plans to set up shop on the West Coast in the third quarter of this year, he said.

Interactive also doesn’t see companies like Knome and Omicia, which also offer tools for genome interpretation and annotation, as competitors since they operate under a different business model focused on providing services.

"We only provide software components; we are not a genetics services company," he said.

Meanwhile, a company like BioBase, which provides some of the annotation data used in Alamut and Alamut HT, isn't a threat because its offerings aren't designed for use within analysis pipelines, Blavier said.

Nor does Interactive expect to compete with its new partner Cartagenia, which markets software for variant interpretation and annotation that has some overlapping capabilities.

Cartagenia, which recently launched a version of its Bench Lab software called Bench Lab NGS that is geared toward clinical laboratories, is partnering with Interactive to integrate its new release with Alamut to provide visualization capabilities and an analytical engine for genetic mutations (BI 3/30/2012).

Cartagenia's offerings lack the breadth of annotation found in Alamut HT and the visualization capabilities of Alamut, Blavier pointed out. On the other hand, he noted that Cartagenia's Bench Lab NGS provides data management features that are lacking in the Alamut suite.

As a result of these differences, "it makes sense for us to cooperate," he said.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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