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GenomeQuest and INRIA collaborate on genome mapping technology for multi-genome analysis
by Jeffrey Bouley  |  Email the author


WESTBOROUGH, Mass.—GenomeQuest and INRIA recently announced the integration of the GASSST technology into the GenomeQuest sequence data management (SDM) platform. Licensed by GenomeQuest from INRIA–or the French national institute for research in computer science and control— GASSST is an open-source genome read mapper designed to maintain accuracy and high-performance as datasets scale to billions of reads with lengths beyond 100 nucleotides.

GenomeQuest and the mapping team at INRIA collaborated closely on the six-month integration project, and GASSST was built into the GQ-Engine—the sequence database engine at the heart of GenomeQuest. As a result, the GASSST mapper inside the GQ-Engine provides the following features: Reportedly supports reads from all sequencing technologies; handles all read lengths from ultra-short to very-long reads, with a variable number of errors, and no restrictions on the number of indels; maps to any kind of reference, from mRNAs to complete genomes, including contigs, without the need of pre-built, static indexes; and is high-performance and scalable to next-generation sequencing (NGS) and multi-genome analysis in commercial data centers.

"Our priority is to enable multi-genome analysis at NGS resolution for our users. In this demanding environment, mappers must maintain high accuracy as projects scale to large and widely heterogeneous collections of datasets," notes Jean-Jacques Codani, GenomeQuest's chief scientific officer, in the news release about the deal. "After an exhaustive evaluation, GASSST not only met this top requirement but its elegant design proved a strong structural and performance fit into our platform. We're very excited about the integration and feel that the combination will accelerate the advance of GenomeQuest users and their organizations to multi-genome analysis."

Codani tells ddn Online that working with INRIA was not only the right choice for technical and practical reasons, but also an easy and natural fit. After all, he says, GenomeQuest was originally founded at the company Gene-IT, and Gene-IT spun out from INRIA in 1999. The core technologies at GenomeQuest and INRIA remain quite similar, therefore, and although some relationships had become outdated, Codani says he had kept in touch with many people at INRIA over the past dozen years.

"This collaboration did not just come out of the blue," Codani points out. "There has been exchange informally over two years about ideas, principles and concept as a peer-to-peer exchange, so when Philippe started coming in and presenting concepts and really implementing ideas, it turned into a collaboration and in our evaluations of other potential partners, it was clear this was the most fitting technology for us."

"Philippe" would be Philippe Gesnouin, technology transfer associate for the life science market at INRIA, who tells ddn Online, "Things do not occur randomly. There were parallel tracks at INRIA and GenomeQuest, things going on for one or two years and then a time came when the technology from INRIA was maturing and the timing with needs of commercial companies matches up, so we decided to 'officialize' the technical and scientific discussions we had been having with GenomeQuest as a collaboration. They are a good fit with us because they are very good with technology transfer."

"For us, it is a crucial point to make sure that whatever is done, useful applications get transferred to the industry, and GenomeQuest is a perfect target to do that," Gesnouin adds. "And talking about history between our organizations, Jean-Jacques and I also worked together on the first French genome project in the early '90s."

Dominique Lavenier, GASSST scientific leader, also notes, in a prepared statement, "The integration of GASSST into a broad industry platform like GenomeQuest is a very gratifying and important step for our team and organization. It allows us to directly contribute to and participate in the larger world of comparative genomics, multi- genome analysis, and personalized medicine research. And the expansive feedback will be fundamental to keeping GASSST as a technology leader in mapping accuracy and performance."

These capabilities are available as a deployed solution or using the GenomeQuest hosted service.  The hosted service, based on a joint GQ-SGI architecture, is now processing hundreds of deep coverage genomes per month, the two organizations note. GenomeQuest and INRIA have agreed to continue their collaboration with efforts focused on GASSST performance optimization inside GenomeQuest.  

"More broadly, we'll continue to avidly support and engage the open source community—their work is critical to the progress of genomics and continued leadership of GenomeQuest," Codani says.

"The relationship has been a clear win-win," Gesnouin says. "Our open-source, enabling technology has advanced the GenomeQuest product while their platform and commercial support will clearly expand the application and rewards of our work."

This announcement follows this month's announcement by GenomeQuest and Ingenuity that the two companies are partnering to support next-generation sequencing workflows specifically targeted for personalized medicine research. Specifically, the companies will integrate GenomeQuest's SDM platform with Ingenuity's IPA software. The aim of that effort is to allow researchers to seamlessly exchange gene information, perform interactive analysis, and create and test hypothesis across the domains of genome sequencing and biological pathways.

Code: E02091101



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