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Taking the next step together
February 2011
by Jeffrey Bouley  |  Email the author


WESTBOROUGH, Mass.—GenomeQuest Inc. and Redwood City, Calif.-based Ingenuity Systems Inc. recently embarked upon a partnership in which they will work to support next- generation sequencing (NGS) workflows specifically targeted for personalized medicine research, primarily by integrating GenomeQuest's Sequence Data Management (SDM) platform with Ingenuity's IPA software. 
This integration will, they indicate, result in the ability of researchers to much more seamlessly exchange gene information, perform interactive analysis and create and test hypotheses across the domains of genome sequencing and biological pathways.
"Biological context is absolutely critical to deriving insights from NGS datasets.  This partnership removes a major data analysis hurdle for our common customers in personalized medicine research," said Dr. Doug Bassett, Ingenuity Systems' chief scientific officer and chief technology officer, in a Jan. 5 news release about the deal. "By integrating SDM and IPA, researchers can take NGS experimental results and place them into known and predicted biological contexts that include biological processes, functions, diseases, pathways, compounds and relationships. This creates a fast and efficient way for researchers to move from a list of genes, isoforms or variants to high-value discovery 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 customers in terms of who was using their products and what those customers needed, but they saw them at different points.
"Where our technology stops is exactly where Ingenuity begins," notes Resnick. "We both realize that one of the biggest markets for next-generation sequencing is personalized medicine, and to get there we have to take aggressive steps in the direction of actually truly understanding the biological interactions and implications."
The "name of the game in personalized medicine research," he adds, is to identify and validate targets for stratification and the integration of the two companies' products will help researchers use multi-genome analysis and comparative datasets to not only enrich their data but to contract those data to the most promising targets—then, armed with pathways analysis and biological process tools, validate and narrow these targets or generate new hypotheses.
"Researchers can have high confidence in these contextual studies because they are leveraging the manually reviewed biological findings that Ingenuity curates from the peer-reviewed literature," Resnick said in the news release about the deal.
Bassett tells ddn the two companies have had a good relationship for years, which made entering into this partnership very natural, and he looks forward to what they can accomplish together.
"With this formal collaboration, it's a long-term, multi-year deal, and I feel like even though we're unlocking significant value for customers early, there is still a lot of exciting work to do together over the coming years to make this space really hum," he says.
The companies note that the integration of SDM and IPA will be available in the GenomeQuest RNA-Seq and multi-genome analysis workflows and that the integration is built on the respective application platforms—the GenomeQuest three-level application programming interface that provides complete access to all functionality and data at the sequence engine, workflow and user presentation levels, and the IPA Integration Module which provides direct links to all content and analysis capabilities within IPA.
Code: E021111



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