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Complete Genomics Offers Commercial, Free Versions of New Variant Analysis, Interpretation Software

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Complete Genomics has launched a commercial, Amazon-based application for the iPad that will enable customers of Complete's sequencing service to visualize, analyze, and annotate genomic variants.

The company later this year plans to launch a web-version of the tool, called Genome Voyager, that will "closely mirror" the iPad app initially but will then mature to include administrative capabilities and more "advanced analysis," Julie Adams, Complete's vice president of product management, told BioInform. The company is also offering a free version of the iPad app with limited capabilities to non-customers.

Both versions of Voyager offer pre-loaded genomes from Complete's previously published 69-genomes dataset, which includes data from Yoruban and Puerto Rican trios and a diversity panel representing unrelated individuals from nine populations. It includes a genome browser that lets users visualize things like copy number variations and loss of heterozygosity, and filtering capabilities to help users find variants by gene panels and annotations. Its annotations follow Human Genome Variation Society standards and users can cross-reference annotations from multiple databases including the single nucleotide polymorphism database and the database of genomic variants.

Other features include the ability to mark interesting variants so that users can find them again easily, and the ability to label pathogenic variants. Through so-called community assessments, users can share their results and give feedback on others' findings. These assessments are included with each variant thus providing an additional source of information to future users.

Complete is offering Voyager to its sequencing customers to both explore pre-loaded genomes and analyze variants in their own sequence data and to share their results with colleagues, Adams said. She also said the pricing for the Genome Voyager's use is rolled into customers' sequencing costs but declined to provide specifics. It's also unclear whether the cost of variant analysis using the web-based version of the tool — which should be available within two to three months — will differ significantly from the iPad app. "That remains to be seen," Adams said.

Complete is also making available a free limited-functionality version of Voyager to non-customers with the hope of improving the body of knowledge on genomic variants and ultimately, helping to move whole-genome sequencing closer to clinical use, according to Adams.

One of "the big barriers" to adopting WGS in the clinical setting is the "aggregation of known knowledge," Adams said. Currently, knowledge about variants is "a moving target; new discoveries are happening, [there is] tons of literature out there, but they are not always concordant with each other," she said. "I think there is a place for the community to come together … and to collaborate on it and thereby improving the knowledge. So, that’s one of the key elements of what we are providing in Voyager right now.”

Interested researchers can request access to the free version of the platform by filling out an invitation form provided by the company. If they are accepted, they can then visualize and analyze pre-loaded genomes from the 69-genomes dataset but they can't use the tool to study their own data.

“By publishing genomes and making them available through Voyager, our goal is to enable more people … to become familiar with analyzing and interpreting whole human genomes,” Adams told BioInform. “If you have access to bioinformaticians, you can do the analysis yourself … if you don't, analyzing and interpreting whole human genomes is out of reach.”

Free users will also able to share information pertaining to the meaning of variants in the data with colleagues within and outside the tool's community.

"One of the things that we have done with Voyager is we’ve integrated it with ClinVar" among other resources, Adams said. "Our plans are when you start to create assessments and really start to do genome interpretation within the tool you would then be able to easily publish out to those types of sources." Users can control what information they share publicly, she added.

Voyager seems similar to Ingenuity Systems' variant analysis software, one of several third-party commercial tools that Complete's sequencing customers have access to as a result of an earlier agreement that lets Complete offer a sequencing services bundle that includes six months of access to the Ingenuity Variant Analysis software (BI 7/27/2012). Adams declined to comment directly on how Voyager's launch could affect her company's pact with Ingenuity. She did say that both firms are "in discussions" around "how we might partner going forward on Genome Voyager."

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