Canada among world's largest genome sequencing sites with $58M partnership

By Debbie Lawes

British Columbia's $8.3-million investment this month in next-generation genomics equipment represents the final tranche in a $58-million collaboration that moves Canada's academic sector into the global top five for DNA sequencing. Canada's Genomics Enterprise (CGEn) has also created the largest genome sequencing platform in Canada by linking three research centres affiliated with the Univ of British Columbia, Univ of Toronto and McGill Univ (see list). By sharing R&D equipment and know-how, the centres say the move will reduce redundancies within experiments and accelerate the study and diagnosis of autism, autoimmune diseases and cancer.

The collaboration links people, equipment and computing power to drive down the cost and time of sequencing genomes at a scale required for large population-based studies.

"This new equipment allows us to conduct this sequencing across multiple jurisdictions, while at the same time being able to share a lot of the research and development costs and share the research protocols," says Dr Steven Jones, head of bioinformatics and associate director of the Michael Smith Genome Sciences Centre. "If we weren't able to get this new generation of machines I think Canada would have had to shut up shop in terms of being a genome sequence-generating country."

The Canada Foundation for Innovation (CF) contributed $23.3 million to CGEn, matched by grants from the BC, Ontario and Quebec governments. In-kind contributions in the form of equipment discounts were provided by gene-sequencing giant Illumina Inc. The company's HiSeq X machine is able to sequence entire human genomes in assembly line fashion at a cost of about $1000 each — the much-touted price point needed to make personalized medicine a clinical reality.

The last of the 15 HiSeq X machines were installed in March, providing the three centres with a combined sequencing capacity of over 27,000 human genome equivalents per year—five times more capacity than previously. The platform also includes data processing (nearly 19,000 compute cores) and storage (over 20 petabytes). An agreement with Compute Canada enables access to additional computational resources.

The equipment "means we can undertake the type of population-based studies that are happening around the world," says Jones. The UK and US, for example, have committed to sequence 100,000 and one million citizens respectively. Mark LePage, president and CEO of Genome Canada, expects to see projects involving as many as 5,000 Canadians in their next health competition in 2017.

Illumina has also lifted a licensing condition that limited the equipment's use to human genomes. Researchers can now use the sequencers for plants, livestock and other non-human species.

LePage says Canadian scientists are particularly well placed to take advantage of this new capability. Where many countries have separate research programs for humans, agriculture and animals, Canada "was a bit different in that we integrated all of that under one roof". He says this approach could give Canada an early lead in genomics-driven agricultural and natural resources research.

CGEn's main focus, however, will be on human studies that benefit Canadians. "Here in BC, we're investing a lot of effort in using the platform to understand the tumors that arise within patients of BC and how that understanding of the genetics of the tumor can impact how we more accurately determine which drugs, for instance, will be most appropriate for those tumours," says Jones.

Perhaps the greatest hope around genetic testing is its promise to rapidly diagnose disease, something Jones' centre is already doing in collaboration with the Children and Women's Hospital in Vancouver. "What we're doing in BC has been world leading in the ability to do human genome (sequencing) as a way to augment the clinical decision making of an oncologist."

More than 500 people work at the Vancouver, Toronto and Montreal sequencing sites, including wet-lab technical staff, informatics personnel, administrative and management, embedded trainees, and project researchers. The three centres are the most established and largest of 10 sequencing platforms supported by Genome Canada.

"Even by global standards each of these centres is large," says LePage. "Until now they have been working in an environment where each was big enough to have informal linkages, but as we go forward, we're looking at projects that may need to be done on two or three platforms at a time ... To do that you need to ensure the platforms are harmonized and standardized. The procedures are very similar and the data is interchangeable."

Growing demand for computing resources

With sufficient sequencing capacity now in place, Canada's next big challenge is ensuring there is enough compute and storage capabilities to manage all these data.

"With next-generation sequencing technologies revolutionizing the life sciences, data processing and interpretation, rather than data production, has become the major limiting factor for new discoveries.

In this context, the availability of advanced research computing resources has become a key issue for the genomics community," Canada's four largest genome centres warn in a March 1 white paper submitted as part of a Compute Canada consultation feeding into its request for new Canada Foundation for Innovation funding (R$, Dec. 21/15).

To meet demand over this period, the centres say computing resources will have to double every two years and online disk and tape backup resources will have to triple.

Compute Canada says the medical, biological and life sciences represent their fastest growing user community. Demand for advanced research computing was up 26% over the past year, and is forecast to surpass the storage needs of the physics community by 2020

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