NSERC and partners fund cloud collaboratory to enhance value of cancer genome data

Slashes time required for analysis

A novel project to help manage and manipulate petabytes of data generated by genomics cancer researchers while respecting the privacy of patients is receiving $7.3 million from a group of federal research funding organization. Funding for the Cancer Genome Collaboratory (CGC) is led by the Natural Sciences and Engineering Research Council (NSERC) which is providing $3.1 million through its rarely used Discovery Frontiers program.

Genome Canada is committing $2 million to the venture, supplemented by $1.3 million from the Canada Foundation for Innovation and $900,000 from the Canadian Institutes of Health Research.

CGC will draw on data generated by the International Cancer Genome Consortium (ICGC) — the world's largest and most comprehensive cancer genome dataset — which is managed and analyzed by the Ontario Institute of Cancer Research (OICR). Participating institutions include the Univ of Toronto, McGill Univ, Univ of Ottawa, Univ of British Columbia, Simon Fraser Univ and the Univ of Chicago.

The latter is also contributing $500,000 worth of in-kind assistance in the form of data and is working in conjunction with OICR on the technical aspects of the collaboratory's hardware and software infrastructure.

By utilizing customized metadata tagging, data provenance tracking and workflow management software, researchers will be able to dramatically reduce the time required to execute complex analytical pipelines, create reproducable traces of each computational step and share their results.

Current practices require weeks of downloading and analyzing terabytes of data. With the CGC, researchers simply upload their analytic software into the cloud, execute the software and securely download the results in a fraction of the time.

"There's limited access to the data right now so we'll be making use of existing open source tools that enable cloud computing and integrate and customize those tools as well as providing management tools," says Dr Lincoln Stein, head of the OICR's informatics and bio-computing program. "The collaboratory responds to customer complaints about our static repository. We have a plan for the management of personal patient genomic data, developing protocols for applying for and using data in an ethical fashion."

Industry partners to date include InterTrust, Sunnyvale, CA, which will develop CGC's legal and ethical framework, and Sage Bionetworks, Seattle WA, which will provide the data provenance tracking system.

"I'd like to leverage the collaboratory to add new features and bring in more partners," says Stein, adding that any new partners would have to secure their own funding.

The competition won by the CGC is only the second call for proposals under the Discovery Frontiers program. Established in 2011, it previously awarded $4 million over four years for the Northern Earth System Research project.

"Discovery Frontiers is relatively small but fairly significant in terms of the size of the grants," says Dr Pierre Charest, NSERC's VP Research Grants and Scholarships .

"This is a key funding opportunity for large teams of researchers to do discovery research. There are few programs at NSERC like this," says Dr Elizabeth Boston, director of NSERC's Mathematical, Environmental and Physical Division

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