Taking the next step together

WESTBOROUGH, Mass.—GenomeQuest Inc. and Redwood City, Calif.-basedIngenuity Systems Inc. recently embarked upon a partnership in which they willwork to support next-generation sequencing (NGS) workflows specificallytargeted for personalized medicine research, primarily by integratingGenomeQuest's Sequence Data Management (SDM) platform with Ingenuity's IPAsoftware.

This integration will, they indicate, result in the abilityof researchers to much more seamlessly exchange gene information, performinteractive analysis and create and test hypotheses across the domains ofgenome sequencing and biological pathways.

"Biological context is absolutely critical to derivinginsights from NGS datasets. Thispartnership removes a major data analysis hurdle for our common customers inpersonalized medicine research," said Dr. Doug Bassett, Ingenuity Systems'chief scientific officer and chief technology officer, in a Jan. 5 news releaseabout the deal. "By integrating SDM and IPA, researchers can take NGSexperimental results and place them into known and predicted biologicalcontexts that include biological processes, functions, diseases, pathways,compounds and relationships. This creates a fast and efficient way forresearchers to move from a list of genes, isoforms or variants to high-valuediscovery outcomes like identifying novel disease-causing variants,prioritizing drug targets and generating testable hypotheses."

Bassett and GenomeQuest CEO Richard Resnick both tell ddn that they saw a strong overlap among their customersin terms of who was using their products and what those customers needed, butthey saw them at different points.

"Where our technology stops is exactly where Ingenuitybegins," notes Resnick. "We both realize that one of the biggest markets fornext-generation sequencing is personalized medicine, and to get there we haveto take aggressive steps in the direction of actually truly understanding thebiological interactions and implications."

The "name of the game in personalized medicine research," headds, is to identify and validate targets for stratification and theintegration of the two companies' products will help researchers usemulti-genome analysis and comparative datasets to not only enrich their databut to contract those data to the most promising targets—then, armed with pathwaysanalysis and biological process tools, validate and narrow these targets orgenerate new hypotheses.

"Researchers can have high confidence in these contextualstudies because they are leveraging the manually reviewed biological findingsthat Ingenuity curates from the peer-reviewed literature," Resnick said in thenews release about the deal.

Bassett tells ddn thetwo companies have had a good relationship for years, which made entering intothis partnership very natural, and he looks forward to what they can accomplishtogether.

"With this formal collaboration, it's a long-term,multi-year deal, and I feel like even though we're unlocking significant valuefor customers early, there is still a lot of exciting work to do together overthe coming years to make this space really hum," he says.

The companies note that the integration of SDM and IPA willbe available in the GenomeQuest RNA-Seq and multi-genome analysis workflows andthat the integration is built on the respective application platforms—theGenomeQuest three-level application programming interface that providescomplete access to all functionality and data at the sequence engine, workflowand user presentation levels, and the IPA Integration Module which providesdirect links to all content and analysis capabilities within IPA.