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World of Genomics: Canada

Article first published by Shannon Gunn, August 2021. Updated by Lyndsey Fletcher, May 2024. With thanks to Rob Annan and Genome Canada.

For the latest in the World of Genomics series, we head over to Canada. Canada has a long history of breakthroughs in genetics, from the discovery of stem cells and the T-cell receptor to the identification of genes involved in cystic fibrosis and early-onset Alzheimer’s disease. There is an active Canadian research community addressing key questions in genetics as well as ongoing efforts to disseminate information among the workforce and public. Canada is also transforming the patient healthcare experience through the integration of a precision health strategy. Plus, we share some insights from Rob Annan, CEO of Genome Canada, who will be joining us at The Festival of Genomics and Biodata on June 12th-13th.

The population of Canada

Located in North America, Canada is the world’s second largest country. It was originally inhabited by Aboriginal peoples, until French and British immigrants colonised the area in the 17th century. Over the last 60 years, immigration has continued to flourish with people arriving from every corner of the globe.

It is expected that the diversity of Canada’s population will increase significantly in the next two decades. In fact, it is predicted that by 2031, between 25% to 28%  of the population will be born overseas. Studying the population of Canada has the potential to provide great insights into indigenous populations as well as that of immigrants. In fact, a study revealed that the average Canadian has more continental European DNA than the average British individual.

Geographic and demographic information

Summary statistics:

  • Land area: 9,984,670 km2
  • Gross domestic product (GDP):
    • Total: $2.13 trillion (2022 estimate)
    • Per capita: $54,917 (2022 estimate)

Population statistics:

  • Population size: In 2024, the total population size of Canda was estimated to be 40,769,890.
  • Birth rate: In 2021, the crude birth rate was 10 per 1,000 people.
  • Death rate: In 2021, the crude birth rate was 8 per 1,000 people.
  • Infant mortality rate: In 2021, the crude infant mortality rate was 4 per 1,000 people.
  • Average life expectancy: The average life expectancy in 2021 was 83 years. 
  • Ethnicity: Aboriginal peoples, English and French settlers are the original founding pillars of Canada. Over centuries, immigration has made Canada more diverse with arrivals from many European countries. In the 2016 census, 32.3% of Canadians considered their ethnic origin to be Canadian. Other major groups recorded were English (18.3%), Scottish (13.9%), French (13.6%), Irish (13.4%), German (9.6%) and Chinese (5.1%). Canada’s aboriginal people are growing at twice the national rate.

Healthcare system

Canada has a publicly funded, universally accessible healthcare system. Access to healthcare in Canada is based on need rather than ability to pay. Their system, known as Medicare, was born in one province in 1947. It then spread across the country and eventually was harmonised through standards in the Canada Health Act of 1984. Rather than having a national healthcare plan, healthcare in Canada is based on its 13 provinces and territories (each of which has its own unique health insurance plan). Like many other countries, the ageing population and costs of advanced medical technology has put pressure on Canada to control health expenditure. As a result, the country was at one point forced to ration drugs, which led to delays and poor coverage in the provision of cutting-edge treatments. The Canadian healthcare system also suffers from long treatment waiting lists, which has been worsened by a shortage of personnel and equipment. While there are some problems in the system, the Canadian healthcare system is typically well regarded.

Health priorities

According to 2019 statistics, cancer was the leading cause of death in Canada, accounting for a total of 80,152 deaths that year. The second leading cause of death among both men and women was heart disease. Surprisingly, the third leading cause of death was accidents. Suicide was also in the top ten leading causes of death in Canada, affecting males more than females. It has been reported that one in three Canadians live with at least one of the following chronic diseases: cancer, diabetes and mood and/or anxiety disorders.

Health Canada releases a new departmental plan each year. In the 2024-2025 plan, there was a strong emphasis on improving access to dental care, modernising health systems, expanding services in rural areas and providing better mental health treatment, among other key priorities. The nation is also investing significant amounts into care for the elderly.

Genomic Medicine Capabilities

The use of medical genetics in Canada started with Madge Macklin, who moved to Canada in 1921 and worked at the University of Western Ontario. Here, she coined the field’s name in 1932. Despite her participation in the eugenics movement, Macklin is still considered the ‘founding mother’ of medical genetics. From then, the field took hold, from the opening of the first genetic counselling clinic in 1947 to recognition by the Royal College of Physicians and Surgeons (Canada) of medical genetics as a free-standing medical speciality in 1989.

Canada has one of the longest-standing genetics professional speciality organisations (The Canadian College of Medical Geneticists). It is also one of the few countries that offer specialised training, including a Master’s level degree for genetic counselling.

Genetic testing in Canada is typically performed in provincial laboratories or outside of the country. Most genetic centres in Canada are primarily linked to academic settings. With genomics becoming more prevalent, there have also been several efforts to develop more extensive patient and family information i.e., the Genetics Education Project.

Newborn screening for phenylketonuria was first introduced in 1963 in Prince Edward Island and expanded to the rest of the country by 1970. Congenital hypothyroidism was added throughout the country in the mid-1970s. Since then, variations have emerged across provinces and territories.

The Society of Obstetrics and Gynecology of Canada recommends that all pregnant women should be offered a range of prenatal screening tests to identify pregnancies at risk of specific chromosome abnormalities and open neural tube defects. These tests were previously only offered to women 35 years and older but have now been extended to all age groups. Screening practices and performance parameters differ across jurisdictions. Uptake also varies by maternal preferences, provider practices and maternal sociodemographic characteristics.

Despite the great promise that genome editing techniques such as CRISPR/Cas9 hold, ethical and social concerns have restricted their use in Canada; the country has some of the most restrictive gene editing laws in the world. For example, under the Assisted Human Reproduction Act of 2004, gene editing in inheritable genes is a criminal offence, punishable by up to 10 years in prison.

Notable Organisations and Companies

  • Genome Canada: Founded in 2000, Genome Canda is a not-for-profit organisation that aims to act as a catalyst for developing and applying genomics to create benefits for Canadians. There are currently six regional genome centres in Canada that receive funding from Genome Canada: Genome British Columbia, Génome Québec, Ontario Genomics, Genome Alberta, Genome Prairie and Genome Atlantic.

We had the pleasure of sitting down with Rob Annan (CEO, Genome Canada) recently, who discussed the organisation’s mission and goals.

“Genome Canada was created just over 20 years ago by the Government of Canada, as an independent not-for-profit. So, we are not part of Government, we are in fact an independent, national organisation set up to lead Canada’s strategy on genomics, in particular, to unlock the potential of the science and create social benefit. We operate as a national organisation, we work with six regional partners based in different parts of Canada, working closely with the provinces.

Our mission is to coordinate large-scale, big picture genomic research projects that  create tangible benefit for society. Interestingly, unlike many genomics organisations worldwide, we do not only operate in the world of health. About half of our portfolio is in the health space, and the other half is in sectors like agriculture, natural resources, and the environment. If it has DNA, we work with it.We coordinate collaborative research projects involving academic researchers and government researchers, as well as companies and not-for-profits working across the country. So, these really are big picture collaborative projects, working across a variety of different sectors.

The other part of our mission that I wanted to highlight is that, while we work a lot on genomics technology and genomic science, a big part of our work is also in the social sciences. We work in an area that we describe with the acronym GE3LS, meaning genomics, and its ethical, environmental, economic, legal, and social implications. We have a philosophy of inclusive genomics, where we’re really trying to ensure that all of our projects not only include representation from the different populations in Canada, but also that the benefits that flow from these projects are going to be equitably shared.”

  • The Canadian College of Medical Geneticists (CCMG): The CCMG is one of the oldest genetics specialty organisations, credentialing clinical and laboratory geneticists since its inception in 1976.
  • The Ontario Institute for Cancer Research (OCIR): The OICR is a not-for-profit organisation established in 2005 with a focus on the prevention, early detection, diagnosis and treatment of cancer. 
  • The Centre for Applied Genomics: This genome centre was founded in 1998 and is based in the Research Institute of The Hospital for Sick Children, and is also affiliated with the University of Toronto. Research at TCAG focuses on the genetic and genomic basis of human variability, health and disease, with an emphasis on the use of NGS and bioinformatics support.
  • The Structural Genomics Consortium (SGC): SGC is a public-private-partnership founded in 2003 focussed on elucidating the functions and disease relevance of all proteins encoded by the human genome.
  • DNA Genotek Inc.: DNA Genotek Inc. is a leading provider of products for biological sample collection, stabilisation and preparation that was established in 1998.

Notable projects

  • Canadian COVID-19 Genomics Network (CanCOGeN): Launched by Genome Canda in April 2020, CanCOGeN aims to establish a network for large-scale SARS-CoV-2 and human host sequencing data to track viral origin, spread and evolution, as well as to characterise the role of human genetics in COVID-19 disease.

Rob also shared with us some highlights from Genome Canada’s work, during the pandemic and beyond.

“Of course, we have 25 years of really exciting work that we’re very proud of. But if you think about the most recent work that we were engaged in, obviously COVID was an enormous challenge here as it was everywhere. It was a challenge not only for the reasons that we all shared – in terms of trying to track in real time the development of a pandemic – but it also got to the core of some of the challenges that we face in Canada: data sharing, data mobilization and so on.

So, we led the formation of a national network called the Canadian COVID-19 Genomics Network, which continues to live on now and is evolving into a broader surveillance tool, really working collectively with public health agencies, as well as hospitals and university researchers across Canada, to keep an eye on, not just COVID, but also other emerging threats, including things like antimicrobial resistance. This kind of surveillance work remains one of the areas of focus.

However, coming out of the crisis point of the pandemic, we did pick up some of the other areas where we’ve been very active, including a slower moving crisis, but one no less severe, when it comes to climate. And last year, we launched a portfolio of projects designed to use genomic tools to mitigate the impacts of our agricultural systems on climate. We call this our Climate Smart Agriculture Initiative. We’re funding a little more than a half dozen projects across the country, which are working together to develop both data and knowledge mobilisation tools, to help use the tools that we’re working on and developing in genomics to address some of the big issues around climate. We also have a large-scale national health data initiative that we’re just preparing now – I look forward to talking to you a little bit more about that at The Festival of Genomics and Biodata in June.”

  • Personal Genome Project (PGP) Canada: PGP-Canada was launched in 2012 and shares the guiding principles and open consent policy of the parent project in the US. It aims to develop a public dataset of fully annotated genomic information linked to human trait information.
  • The FORGE (Finding of Rare Disease Genes) Canada Consortium: The FORGE Canada Consortium began in 2011 with the objective to rapidly identify genes associated with a wide spectrum of rare paediatric-onset single-gene disorders present in the Canadian population.
  • Genome Canada’s All for One initiative: The All for One initiative aims to improve the health and wellness of Canadians with serious genetic conditions by enabling access to a timely and accurate genomic-based diagnosis. Part of this initiative is a clinical implementation project that will facilitate the uptake of genome-wide sequencing as a standard of care for rare diseases.

Rob Annan also talked to us about the ‘Silent Genomes’ initiative.

“One area where we are increasingly active, and working with a set of really great partners, is in the area of Indigenous genomics. Of course, Canada has a number of Indigenous populations, from coast to coast. And those Indigenous communities in Canada have a difficult and fraught history with medical science. So, we’ve been working very hard with community partners, both Indigenous and non-Indigenous partners, to address some of those issues and ensure that Indigenous communities in Canada are able to benefit from the potential that genomics brings on the health side, in particular, but not only on the health side. We are one of the supporters of an important project in Canada called Silent Genomes, which seeks to establish a biobank and associated data assets for Indigenous communities, starting in northern British Columbia. We partner with the Summer Internship Program in Indigenous Genomics to develop talent and expertise among young Indigenous scholars in genomics.

We work with partners globally on issues in health, certainly when it comes to data sharing, but also in areas, for instance, like environmental genomics. Digital sequence information is a very important topic when it comes to benefit sharing, and threats around what we might consider something like bio-colonialism. So, we’re trying to make sure that we have a very inclusive approach to these subjects. We work withpartners in Canada and abroad to make sure that these issues are front and foremost in in our strategy.”

Notable individuals

There are many individuals born or immigrated early to Canada who have had a significant impact on the genetics field. Below are just a few of these individuals:

  • Charles Scriver (1930-): Scriver is a Canadian paediatrician and biochemical geneticist who has made many important contributions to our knowledge of inborn errors of metabolism. He also led in establishing a nationwide newborn metabolic screening program.
  • Stephen W. Scherer (1964-): Scherer is a Canadian scientist who alongside Lap-chee Tsui founded Canada’s first human genome centre – TCAG. His discoveries also led to the initial description of copy number variations (CNVs) and the frequency of these events. Scherer and colleagues also launched the Personal Genome Project Canada in 2012.
  • Johanna Rommens: Rommens is a Canadian geneticist who was on the research team which identified and cloned the CFTR gene (responsible for causing cystic fibrosis).
  • Phyllis McAlpine (1941-1998): McAlpine was a Canadian geneticist and pioneer in mapping the human genome. She also served as Chair of the HUGO Gene Nomenclature Committee, recognising the importance of standardised nomenclatures.
  • Tak Wah Mak (1946-): Mak is a Canadian medical researcher, geneticist, oncologist and biochemist. He became widely known for his discovery of the T-cell receptor in 1983 and the discovery of the function of CTLA-4 in 1995.
  • Thomas J. Hudson (1961-): Hudson is a Canadian genome scientists known for his leading role in the generation of physical maps of the human and mouse genomes as well as his role in the International HapMap Project.
  • Carolyn J. Brown (1961-): Brown is a Canadian geneticist and Professor at the University of British Columbia. Brown is known for her work on X-chromosome inactivation, having discovered the human XIST gene in 1990.

Next steps

With the breadth of diversity and the minds of some of the greatest geneticists, Canada is the perfect place to study genomics and implement genomic medicine. Nonetheless, several challenges remain to ensure that genomics is deployed appropriately. For the benefits of genomics to be effective within clinical practice, the genomic literacy of healthcare professionals must be advanced. In addition, access to clinical genomic testing across Canada is currently inconsistent, which is often correlated with socioeconomic and/or regional differences.

We spoke more to Rob Annan about Genome Canada’s strategic goals in the coming years.

“We are really focused right now on the issue of data and data sharing. We are focused on the development of large-scale data assets that contribute not just to Canadian innovation and Canadian impact, but global innovation and global impact. We are tackling the challenges around data sharing in genomics health data head on, and that will be a major focus for us over the next several years. But we’re also looking at developing large-scale data assets in agriculture, particularly as a resource to help us deal with the impacts of climate change or heat resistance and drought and so on. As well as surveillance for emerging pathogens and antimicrobial resistance. So, really thinking about data and data coordination is going to be a major focus for us.

We’re also thinking about the intersection of data and AI. Of course, globally, AI is exploding. Canada has significant strengths in AI, a lot of globally leading researchers and institutes in Canada are building at an enormous capacity, and we see genomics as a real feedstock for that AI learning and development. Thinking about the intersection of genomics and AI, I think is going to be really important. And all of this, of course, creates a number of challenges on both the ethical side and the inclusion side. Those are front of mind for us and remain a very important area of focus going forward.”

Continued investment in genomics research and collaborations among academic, industry, healthcare and other partners will not only improve the lives of Canadians but will also help Canada recover and stay competitive in a post-pandemic economy.

References

  • Little J, Potter B, Allanson J, Caulfield T, Carroll JC, Wilson B. Canada: public health genomics. Public Health Genomics. 2009;12(2):112-20.
  • Leeming W. The early history of medical genetics in Canada. Social History of Medicine. 2004 Dec 1;17(3):481-500.
  • Martin D, Miller AP, Quesnel-Vallée A, Caron NR, Vissandjée B, Marchildon GP. Canada’s universal health-care system: achieving its potential. The Lancet. 2018 Apr 28;391(10131):1718-35.
  • Irvine B, Ferguson S, Cackett B. Healthcare Systems: Canada. Civitas, January. 2013.