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New investments launch pediatric precision medicine projects

January 23, 2018
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The Genome Canada’s 2017 Large-Scale Applied Research Project (LSARP) Competition will support six innovative projects led or co-led by investigators at BC Children’s Hospital, an agency of the Provincial Health Services Authority:

Silent Genomes: Reducing health-care disparities and improving diagnostic success for Indigenous children with genetic disease 

 “The Indigenous Peoples of Canada face unique health challenges, inequities, and barriers to health care and typically have poorer health outcomes than non-Indigenous groups. While leading-edge genomic technologies are becoming routinely available to other Canadians, Indigenous people often have little or no access to these technologies, increasing the health disparity gap. Silent Genomes is a game-changing effort to address this inequity, by bringing life-changing genomic diagnosis to children while ensuring Indigenous-led governance over biological samples and health data.” -Dr. Laura Arbour, Investigator and Clinical Geneticist, BC Children’s and Island Health; Professor, Department of Medical Genetics, University of British Columbia. 

Precision medicine, the creation of new precisely targeted therapies with a patient’s genetic information, is poised to revolutionize treatment and care, particularly for children with complex health conditions caused by genetic disease. Significantly, Indigenous Canadian communities (First Nations, Métis and Inuit) are increasingly left behind in this “genomics revolution” and continue to face longstanding barriers to accessing health care.

Silent Genomes will work in concert with Indigenous Canadian communities to change this by:

  • Establishing First Nations, Inuit and Métis-led governance and model policy development for genomic research and clinical care 
  • Bringing state-of-the-art genomic testing to Indigenous children in Canada suspected of having a genetic condition 
  • Creating an Indigenous Background Variant Library (IBVL) of genetic variation from a diverse group of First Nations in Canada that will improve the accuracy of genomic diagnosis by providing necessary reference data
Dr. Arbour leads this project with co-leads Dr. Wyeth Wasserman, BC Children’s and UBC; and Dr. Nadine Caron, University of Northern British Columbia. This project is based at BC Children’s, BC Women’s Hospital + Health Centre and UBC.

Childhood asthma and the microbiome – precision health for life: The Canadian Healthy Infant Longitudinal Development (CHILD) study

 “We’re using powerful genomics technologies to study the connection between the presence of certain gut microbes early in life and the risk of developing asthma in childhood. Our goal is to find a way to identify babies at risk for asthma and treat them so they never develop the condition.” –Dr. Stuart Turvey, Investigator and Director, Clinical Research, BC Children's; and Aubrey J. Tingle Professor of Pediatric Immunology, UBC.

Asthma is the most common chronic disease of childhood, affecting one in seven Canadian children and costing the health care system more than $2-billion per year. Current treatments can manage the symptoms of asthma, but there is no effective way to prevent or cure this dangerous, chronic condition. Previous research from Dr. Stuart Turvey and the CHILD study team found that children who are missing four types of gut bacteria at three months of age are more likely to develop asthma. With this new funding, the team will further this research by using genomic technology to analyze stool samples from infants. The goal is reduce the burden of asthma by creating new diagnostic tools that will identify babies who are likely to develop the condition and develop new treatments that will replace missing gut bacteria to stop asthma before it starts.

Dr. Turvey leads this project with co-leads Dr. Michael Kobor, BC Children’s and UBC; Dr. Sara Mostafavi, BC Children’s and UBC; Dr. Brett Finlay, UBC; and Dr. Padmaja Subbarao, SickKids and McMaster University. This project is based at BC Children’s, BC Women’s and UBC.


Genomic and outcomes database for pharmacogenomics and implementation studies (Go-PGx)

“For kids with cancer, chemotherapy is life-saving but brings with it the risk of life-threatening complications. Through genomic-driven precision medicine, we can identify children at risk for these complications before they are treated. The GO-PGx project will make this testing available at 10 children’s hospitals across Canada, expanding our capacity to predict serious complications and generally making medications safer for our kids”– Dr. Bruce Carleton, Senior Clinician Scientist and Director, Pharmaceutical Outcomes Programme, BC Children's; and Division Head, Translational Therapeutics and Professor, Department of Pediatrics, UBC.

The powerful drugs that treat cancer can sometimes have unintended consequences. Adverse Drug Reactions (ADRs), also known as “side-effects,” can result in pain and disability, interruptions in treatment and even death. Research led by Dr. Bruce Carleton has identified some of the genetic differences that can identify whether a child is at increased risk of developing ADRs and has implemented this predictive test at BC Children’s. The Go-PGx project aims to expand these efforts by:

  • Analysing more than more than 6,125 DNA samples and corresponding clinical data to improve the capacity to test for genetic susceptibility to ADRs
  • Developing educational tools for physicians and families
  • Creating a comprehensive database on ADRs that will be accessible to researchers worldwide
  • Introducing testing for ADRs at 10 pediatric centres across Canada
Dr. Carleton leads this project with co-principal investigator Dr. Colin Ross, BC Children’s and UBC; and Dr. Rod Rassekh, BC Children’s and UBC. This project is based at BC Children’s, BC Women’s and UBC.

GenCOUNSEL: Optimization of genetic counselling for clinical implementation of genome-wide sequencing

“For patients with rare, unexplained disorders and their families, genome-wide sequencing (GWS) can provide much-needed answers but it can also raise a lot of questions. Families need clinical expertise and emotional support to make informed decisions. Genetic counsellors are specialist health care providers with the expertise to lead the integration of genomics into patient care across all areas of medicine. Our project, GenCOUNSEL, will result in increased access, patient satisfaction and cost-efficiency through provision of effective and professional genetic counselling for all Canadians who need it.”–Dr. Alison M. Elliott, Board certified genetic counsellor and Investigator, BC Children’s Hospital; Project Lead, CAUSES Clinic and RAPIDOMICS; Associate Member, Women’s Health Research Institute; Clinical Associate Professor, Department of Medical Genetics, University of British Columbia.

GWS, a powerful genetic test that analyzes a person’s entire genetic make-up to diagnose the cause of genetic disorders will soon be available in Canada. GWS can provide patients with valuable information about their health, but it can generate complex results that are difficult for non-expert health providers to interpret and can reveal disorders or disease risk unrelated to the original reason for testing.

Genetic Counsellors represent the “front line” of medical genetics and their expertise will be particularly vital to families receiving GWS. By providing education, emotional and decisional support to patients and families and guiding them to make informed decisions regarding genetic testing, genetic counsellors help prevent inappropriate decision making that can have devastating health and/or emotional consequences. However, in Canada, there is limited access to genetic counselling, and this issue will become more pressing as GWS becomes increasingly available.

GenCOUNSEL is the first project to look at genetic counselling issues related to the implementation of GWS. It will bring together international experts in genetic counselling, genomics, ethics, law, health services implementation and health economics to determine the best methods for providing genetic counselling and ensure all Canadians have access to this specialized expertise and support. 

Dr. Elliott leads this project with co-leads Dr. Jehannine Austin, BC Mental Health and Addictions Research Institute, BC Children’s, BC Women’s and UBC; Dr. Bartha Knoppers, Centre of Genomics and Policy, McGill University; and Dr. Larry Lynd, UBC, Centre for Health Evaluation and Outcomes Sciences, Providence Health Care Research Institute, and Centre for Clinical Epidemiology and Evaluation, Vancouver Coastal Health Care Research Institute. This project is based at BC Children’s, BC Women’s and UBC.

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

“For many patients with a rare disease, diagnosis is a years-long odyssey involving visits to multiple specialists, invasive testing and fruitless or missed treatments. The C4R-Solve Project will increase access to state-of-the-art genomic and other innovative ‘omics’ testing, giving patients and families with rare diseases long-awaited answers and helping doctors provide the best possible care.” – Dr. Clara van Karnebeek, Investigator, BC Children's; Principal Investigator, Centre for Molecular Medicine and Therapeutics; Affiliate Associate Professor, Department of Pediatrics, UBC.

Over one million Canadians suffer from a rare disease and in one-third of these cases, the underlying genetic cause of the illness remains unknown.  The C4R-Solve Project will increase access to state-of-the-art genomic sequencing and other “omics” technologies, which explore how the different molecules that make up cells operate and interact. Through these efforts, the C4R-Solve Project will speed diagnosis for Canadians with suspected rare genetic diseases and save patients from unnecessary tests and ineffective treatments. The C4R-SOLVE team will work with provincial ministries of health to integrate genomic sequencing into the clinical care of patients with rare disease and build infrastructure and tools to improve rare disease diagnosis and advance the understanding of the underlying mechanisms of these conditions worldwide. C4R-Solve will more than double the capacity to diagnose rare diseases in Canada, improving care for patients by tailoring management to their underlying condition, providing new insights into rare conditions and saving at least $28-million a year in unnecessary health care spending. 

Dr. van Karnebeek is the lead for this project in British Columbia along with Dr. Anna Lehman, BC Children’s Hospital and UBC, and Dr. Sara Mostafavi, BC Children’s Hospital and UBC. Dr. Kym Boycott, Children’s Hospital of Eastern Ontario (CHEO) and University of Ottawa, leads this national project along with Dr. Michael Brudno, SickKids Research Institute and University of Toronto, and Dr. François Bernier, Alberta Children’s Hospital and University of Alberta. This project is based at CHEO. 

PEGASUS-2: Personalized Genomics for Prenatal Abnormalities Screening Using Maternal Blood: Towards first tier screening and beyond

“Families in Canada should have access to state-of-the-art technology, which allows them to get safer, more reliable results about certain genetic disorders earlier in pregnancy. That’s the goal of the PEGASUS-2 project; I’m working with researchers across Canada to make publicly funded non-invasive prenatal screening an option for all pregnant women.” – Dr. Sylvie Langlois, Investigator, BC Children's; Clinical Geneticist, BC Children’s, BC Women’s; Professor, Department of Medical Genetics, UBC and Medical Director, BC Prenatal Genetic Screening Program.

Non-invasive prenatal screening (NIPS) can accurately detect Down syndrome and other chromosomal abnormalities in the first trimester of pregnancy with a simple blood test. Because of its relatively high cost, NIPS is currently only used on mothers who have already tested positive on a less expensive and less accurate test. The goal of the PEGASUS-2 project is to support the use of NIPS as a first-tier test, giving expectant families publicly-funded access to more accurate screening results, earlier in pregnancy. PEGASUS-2 will:

  • Compare the use of NIPS as a first-tier and second-tier test in a large cohort of pregnant women
  • Study the cost effectiveness and ethical, social and legal implications of expanding NIPs screening to conditions other than Down syndrome
  • Provide strategies to promote shared decision-making between couples and health care professionals
  • Further develop the NIPS technology to reduce its costs by 50 per cent and expand its ability to detect other anomalies, as well as ensuring quality control for clinical NIPS testing in Canada and worldwide
Dr. Langlois leads the project with co-lead Dr. François Rousseau, Université Laval. This project is based at Université Laval.