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Genome Canada, Canadian Institute of Health Research to Fund Sequencing of Childhood Diseases

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By Monica Heger

Genome Canada and the Canadian Institute of Health Research said last week that they will jointly fund a program to sequence childhood disease cohorts. Each institution will contribute C$2 million ($1.9 million), and the project will last for about one year, beginning in 2011.

At a workshop this week, representatives from Genome Canada and the Canadian Institute of Health Research met with researchers and clinicians from medical schools and genome centers throughout Canada to discuss the scope of the project, the sequencing technologies to be used, and how the participants will decide which diseases to study.

The project has two overall goals: "to identify disease genes that have to do with heritable childhood diseases, and to demonstrate Canadian proficiency in state-of-the-art genomic technologies," Paul Lasko, the scientific director of CIHR's Institute of Genetics told In Sequence. He said the project will most likely focus on exome sequencing, and will utilize solely next-generation sequencing technology.

A request for applications will be released this week via the Genome Canada website, and applications for the project will be due Oct. 15, with funding released in December, Cindy Bell, the executive vice president of corporate development at Genome Canada, told In Sequence. The agencies plan to award one grant under the program.

Because the project is slated to last about one year, priority will be placed on diseases for which patient cohorts already exist and diseases where there is a good chance of identifying causal genes, or where there is a greater likelihood of developing therapeutics, said Lasko. He added that the diseases studied would likely fall under two main categories: rare, Mendelian diseases and pediatric cancers.

The sequencing will be done at Genome Canada's three science and technology innovation centers: the Genome Sciences Centre in Vancouver, the McGill University and Genome Quebec Innovation Centre in Montreal, and the Centre for Applied Genomics in Toronto. The sequencing technology that is used will depend on what is available at the center doing the sequencing.

The focus will be on whole-exome sequencing, because "we think with the available resources we can look at more disorders," said Lasko. "Although that's not to say that whole-genome sequencing won't be tried for some of the disorders."

Bell agreed: "So far, exome sequencing sounds the most reasonable. But if the case can be made for other techniques to be used, we would certainly consider those."

The C$2 million from Genome Canada will be used to fund the sequencing and bioinformatics analysis, although the funds will not be used for the purchase of new sequencing instruments. CIHR's share will go towards the initial collection of patient data and any downstream validation.

Bell said that the agencies hope to attract additional funders, so the overall budget may be greater than C$4 million. She said that Genome Canada and CIHR have been in discussion with Canada's regional genome agencies, as well as universities, hospitals, foundations, and disease organizations regarding additional funding for the project.

"We certainly would like to expand the resources available for this, and that will be one of our next steps," Bell said.

Both Bell and Lasko said that they anticipate that a small number of consortia would form following this week's workshop, involving research groups from around the country, and that each would submit a formal application. Lasko said that the consortia would likely decide amongst themselves how to prioritize diseases.

Lasko added that the project could be particularly useful for researchers studying diseases in relatively isolated areas in Canada. He said there are some family cohorts of Mennonite and Amish in rural areas of Canada, but that the researchers studying these populations have not had access to genomic technology.

"There are clinicians at some of these smaller centers that have wonderful patient material," said Lasko. And this program would provide the "ability for these folks to access the technology."

While the initial project will last only one year, Lasko said that there could be opportunities to extend the program. For example, Lasko said CIHR's Institute of Genetics will soon launch an RFA on rare diseases that will provide funding for five years, so a group funded under the sequencing project could apply for additional funding to do longer-term functional analyses. Similarly, the Institute of Cancer Research recently launched an initiative on pediatric cancers, said Lasko.

Both Lasko and Bell stressed, however, that the focus of the current initiative is really on the year ahead. "We want to take advantage of what we have in hand in terms of the tissue resources, disease cohorts, and the technology, in order to have an impact as quickly as possible," Bell said.

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