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Montreal's PGx Center Creates 38-TB Storage


As part of its setup for a new Illumina Genome Analyzer, the bioinformatics team at the Montreal-based Pharmacogenomics Centre is ramping up its storage to 38 terabytes to handle data from upcoming sequencing projects by its 25 staff researchers and outside customers.

The Pharmacogenomics Centre will be using Seattle-based Isilon Systems' IQ network-attached storage for its second-generation sequencing operations. The center, a partnership between Université de Montréal, the Montreal Heart Institute, and Génome Québec, faces data storage challenges that many larger sequencing centers have been busily taming. For example, whereas the Ontario Institute for Cancer Research has a "huge" infrastructure, "we're minnows as far as they are concerned," says Christopher Beck, the center's senior bioinformatician. The center mainly does government-funded research, he says, adding that it hasn't gained much Genome Analyzer experience yet. He and his colleagues have completed three runs for research projects plus a few test runs.

The Isilon system "has never come close to even choking a little bit," Beck says, adding it has only processed one sequencer run at a time, with "a couple of terabytes a week" of data. Prior research at the center focused exclusively on SNP analysis using Sequenom's MassArray, the AutoGenomics Infiniti system, and Beckman's SNPstream, and the team is now adding second-gen sequencing projects, Beck says. A cancer sequencing study was slated to begin this month, and new pharmacogenomics projects will include collaborations with undisclosed pharma companies. The center opted for Isilon mainly due to the "zero management aspect," he says. While some institutes have IT support staff and "storage professionals," his group of five bioinformaticians and affiliated genomics researchers are going it alone. "We wanted to go with something that was low maintenance and easy to deploy," he says.

— Vivien Marx

Bioinformatics Notes

Ingenuity Systems has signed a multi-year deal for its Ingenuity Pathway Analysis platform with the Queensland Facility for Advanced Bioinformatics. Ingenuity says that IPA will be one component of a systems biology platform funded by the Australian Research Council in partnership with the Australian Stem Cell Centre and other institutions.

The Jackson Laboratory will use a $2.1 million grant from the National Center for Research Resources to expand the lab's computational facility and hire staff.

The Broad Institute is using Genedata's Screener software platform to manage and analyze high-throughput screening data as part of its participation in NIH's Molecular Libraries Roadmap Initiative.


$67.5 million
Amount NIAID has awarded over five years to four Bioinformatics Resource Centers for Infectious Diseases

Funded grants

$488,261/FY 2009
Techniques for Integrated Analysis of Graphs with Applications to Cheminformatics and Bioinformatics
Grantee: Ambuj Singh, University of California, Santa Barbara
Began: Sep. 15, 2009; Ends: Aug. 31, 2012

This grant will go to support the development of a set of scalable querying and mining tools for graph databases by integrating techniques from databases and data mining.

$150,000/FY 2010
SBIR Phase I: Bioinformatic FPGA Appliance
Grantee: Vincent Natoli, Stone Ridge Technology
Began: Jan. 1, 2010; Ends: Jun. 30, 2010

This project will investigate the technical and commercial feasibility of a bioinformatics computing appliance based on FPGA technology. The company proposes to create an appliance using an open-source algorithm for a feasibility study in order to create a "powerful and optimized engine" for this algorithm that can be operated through a Web interface.

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New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.