Advancing Big Data Science in Genomics Research

In 2013, the Natural Sciences and Engineering Research Council of Canada (NSERC), Genome Canada, the Canadian Institutes of Health Research (CIHR) and the Canada Foundation for Innovation (CFI) partnered on a 2013 Discovery Frontiers call for proposals, focused on advancing big data science in genomics research. This initiative was designed to support the development of tools and methodologies to integrate currently available complex data sets in the fields of ‘omics sciences with each other, as well as with phenotypic data and data from other related fields of biological sciences. It was aimed at building on past and ongoing investments in this area, the most recent being the Bioinformatics and Computational Biology Request for Applications launched in June 2012 by Genome Canada and CIHR.

The result of the Competition was announced April 30, 2014. Federal funding totaling $5.6 million was awarded to the Ontario-led project to support an unprecedented collaboration – both in Canada and internationally – to develop tools that can effectively manipulate vast amounts of data to help find cures for cancer.

Personalized medicine in the treatment of epilepsy (2012)


Every time someone with epilepsy has a seizure there is a risk of brain damage. This is particularly true for children. Unfortunately, today’s anti-epileptic drugs simply don’t work on about one third of patients. The team led by Drs. Patrick Cossette, Berge Minassian and Jacques Michaud will identify genes that are associated with epilepsy and that are predictive of the response to various antiepileptic drugs. This will result in earlier and more effective care and potentially prevent cognitive decline in children. This project is co-led with Genome Quebec.

The microbiota at the intestinal mucosa-immune interface: A gateway for personalized health (2012)


Inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis, are incurable debilitating lifelong diseases that can affect children. Early detection is critical to avoiding complications and improving their quality of life. At the moment, however, there is no single test to determine the presence or type of IBD and the tests that exist are very uncomfortable for children. Drs. Alain Stintzi, David Mack and team are developing a simple, non-invasive approach to detecting IBD that will also be more cost effective. Using cutting-edge technology, the scientists will examine intestinal bacteria to develop better ways of identifying IBD and determining its severity. This work could also lead to new treatment, enhancing the quality of life for children everywhere.

Early detection of patients at high risk of esophageal adenocarcinoma (2012)


Chronic heartburn can damage the lining of the esophagus, leading to a condition known as “Barrett’s esophagus”. Patients with Barrett’s esophagus have a much higher chance of developing cancer of the esophagus. Until recently, the only way to diagnose Barrett’s esophagus was through endoscopy—an uncomfortable and time-consuming procedure. However, a swallowable sponge under development in the United Kingdom allows for quick and painless diagnosis of Barrett’s esophagus in a doctor’s office. The team led by Drs. Lincoln Stein and Tony Godfrey aim to supplement this test with genomic technologies, allowing doctors to follow patients over time to identify and treat those progressing to cancer. Early detection, treatment and even prevention of these cancers could save the healthcare system over $300 million a year.

Autism spectrum disorders: Genomes to outcomes (2012)


Genome Canada and CIHR-funded research has already led to some exciting breakthroughs in our understanding of autism spectrum disorder, a complex condition that affects normal brain development, social relationships, communication and behaviour. Among these breakthroughs is the identification of specific DNA anomalies associated with the illness. Now, Drs. Stephen Scherer, Peter Szatmari and team are going to the next level, aiming to identify the remaining genetic risk factors. This ground-breaking work will mark Canada’s contribution to an ambitious international initiative that aims to sequence and analyze the genomes of 10,000 people with autism spectrum disorder. With a more complete understanding of the genetic elements of autism, doctors will be able to make earlier diagnoses, provide better, more personalized care to patients and reduce the enormous cost autism imposes on our health care system.

Enhanced CARE for RARE genetic diseases in Canada (2012)


Gene mutations cause not only well-recognized rare diseases such as muscular dystrophy and cystic fibrosis, but also thousands of other rare disorders. While individually rare, these disorders are collectively common, affecting one to three percent of the population. It is estimated that as many as half of Canadians with rare disorders are undiagnosed. Drs. Kym Boycott, Alex MacKenzie and team will use powerful new gene sequencing technologies to identify the genes implicated in many of these rare diseases. Besides providing important new understanding into human disease, this project will yield other benefits, including: avoiding invasive procedures, stopping ineffective treatments, developing earlier and better diagnoses, devising more appropriate treatment, and predicting the chances that one of these rare diseases could be passed on to offspring. Once the disease-causing genes have been identified, researchers will test drugs that are currently on the market to identify those that might be effective against these rare diseases.

Care4Rare Canada: Harnessing multi-omics to deliver innovative diagnostic care for rare genetic diseases in Canada (C4R-SOLVE) (2017)


There are more than 7,000 rare genetic diseases in Canada, which have a devastating impact on some one million Canadians and their families: two-thirds of these diseases cause significant disability; threequarters affect children; more than half lead to early death; and, almost none has any targeted treatment. Further, more than one-third of these diseases remain unsolved (their genetic cause is unknown). Building on the work of the Care4Rare Canada Consortium, the C4R-SOLVE project is working to identify the genetic cause of unsolved rare diseases and make genomic sequencing available to Canadians for rare disease diagnosis. Genomic sequencing will speed up the diagnostic process, thereby ending or even preventing years of diagnostic testing and visits to multiple specialists. Providing a timely diagnosis improves the care and wellbeing of patients and their families and reduces unnecessary healthcare spending. Key to C4R-SOLVE’s success will be new sequencing technologies and improved worldwide data sharing. In addition, the group will work with provincial ministries of health to determine how best to include genomic sequencing as a clinical test to diagnose rare diseases, beginning with Alberta and Ontario. In doing so, C4R-SOLVE will more than double our ability to diagnose unsolved rare disease, while building the infrastructure and tools needed to improve rare disease diagnosis worldwide. Accurate and early diagnosis will optimize care, improve the wellbeing of patients and their families, provide new insights into these devastating diseases, and potentially save at least $28 million/year in health-care spending.