Press Release

GenomeQuest and SGI Announce Whole-Genome Analysis Architecture


Westborough, MA and Fremont, Calif.CA, August 4, 2010: GenomeQuest and SGI (NASDAQ: SGI) today announced the immediate availability of the world's first whole-genome analysis (WGA) services for researchers. As a result, pharmaceutical companies, core labs, biotechs, government agencies, and clinics now have direct access to whole-genome processing previously found only inside genome centers combined with comprehensive, self-serve analysis.

The WGA services allow whole-genome/exome research teams to:

  • Store, manage, and compare their sequences and annotations
  • Assemble and align sequences from any instrument
  • Interactively query and analyze their runs and projects
  • Merge and re-analyze with findings from colleagues and public studies
  • Use standard workflows, including Variant Detection, RNA-Seq, and ChIP-Seq
  • Build and query enterprise-wide variant archives, and
  • Integrate with other tools/systems through an all-level API.

"Data analysis is recognized as the bottleneck of whole-genome research. Traditionally, researchers receive static reports for their sequence runs which, at today's volumes, are impossible to analyze and increasingly siloed," said Jean-Jacques Codani, GenomeQuest Chief Scientific Officer. "From its inception, the GQ Engine has provided researchers with rich, interactive reports and the ability to integrate and re-analyze with other work. Now, with SGI's longstanding experience in high-performance computing, we have found the bow that best fits our arrow for WGA scale services."

GenomeQuest and SGI co-developed a software and hardware architecture that is optimized for next generation sequencing and enables whole-genome scale and performance. Based on this architecture, the WGA services are available through the just-upgraded GenomeQuest data center or deployed directly into a customer data center, as may be required by larger accounts, core labs, and clinics.

"Clearly, the storage and computational needs of WGA are massive and unique," said Dr. Eng Lim Goh, senior vice president and chief technology officer at SGI. "Given the complexity of the algorithms and the scale of the data, success in this area requires a careful factoring then optimization across four key parts of the system - software, computational and I/O capabilties, and burstability. We are very excited about the new GenomeQuest center, and applying this enabling blueprint for life science organizations."

The GenomeQuest center was upgraded on May 18, 2010. A major investment, it radically improved the user experience and performance for over 2000 existing commercial and academic users.

"We have observed a radical change in the use of GenomeQuest since the opening of the new center," comments Ron Ranauro, GenomeQuest CEO. "Our personalized medicine research application is processing thousands of exomes per month and will soon scale to over 1000 full-human genomes at deep-coverage."

The SGI-based upgrade includes:

  • Multiple, load-balanced head nodes to service high-volume user requests and interactions
  • Rackable™ XE, server stack of high-performance compute nodes to service highly-parallelized, sequence database comparisons
  • Storage solution featuring high-performance I/O subsystem scalable to Petabytes
  • Housed in a Type II SAS 70 compliant data center with fully redundant hardware and software for 24/7 availability

In related recent news at BIO-IT WORLD, GenomeQuest also announced GQ-PMR, the world's first genomic reference system for personalized medicine-based research. With GQ-PMR, pharmaceutical companies can integrate raw data from public whole genome studies, such as the 1000 Genome Project, directly into their private research. The combination allows research organizations to massively expand sample sizes at virtually no cost and accelerate their transition to molecular-based personalized medicine.

As background, in a July 8, 2010 feature story in USA Today titled "The human genome: Big advances, many questions", Vivien Bonazzi, head of computational biology for National Human Genome Research Institute at the National Institutes of Health, comments, "We're really crying out for the ability to analyze this [output of genome sequencing machines] efficiently and effectively."

Industry Motivation for the GQ-Engine

More on GenomeQuest

GenomeQuest, the leader in sequence data management (SDM) helps genomic researchers and their organizations make great discoveries far faster. Over 160 leading life science companies use GenomeQuest for mission-critical work, including 17 of the top 20 pharmaceuticals.

About SGI

SGI is a global leader in large-scale clustered computing, high performance storage, HPC and data center enablement and services. SGI is focused on helping customers solve their most demanding business and technology challenges.

Visit www.sgi.com for more information.

(c) 2010 GenomeQuest, Inc. GenomeQuest and the GQ-Engine are trademarks of GenomeQuest, Inc. SGI and Rackable are registered trademark or trademarks of Silicon Graphics International Corp. or its subsidiaries in the United States and/or other countries. All other trademarks are property of their respective holders.