CGEn is Canada’s national platform for genome sequencing and analysis, with nodes at The Centre for Applied Genomics at The Hospital for Sick Children (SickKids) in Toronto, the McGill Genome Centre in Montreal and Canada’s Michael Smith Genome Sciences Centre at BC Cancer in Vancouver. CGEn is a Major Science Initiative of the Canada Foundation for Innovation (CFI-MSI) providing world-class infrastructure, services, and expertise since being founded in 2015, and enabling novel research and technology development that would otherwise be impossible within Canada. To date CGEn has generated over 12.6 petabases of sequence data for more than 2,900 research labs, companies, and not-for-profits. To remain internationally competitive, CGEn makes considerable efforts in technology development activities to drive forward innovation and formulate new approaches to genomic science. In turn, this ensures that CGEn continues its optimal support of Canada’s research and innovation ecosystem, while remaining in a ready-state to respond to large-scale genomic opportunities and challenges.

This project focuses on technology development driven by demand from the scientific community and aligned with CGEn’s key existing and emerging service growth areas including (i) Long-read sequencing and associated analysis and interpretation of data, (ii) Single cell genomics to produce data on individual cells from a cell population (iii) Spatial transcriptomics to understand intracellular biology with integrated information, ultimately leading to highly accurate tissue specific cell maps, and (iv) Short-read sequencing focusing on the assessment and validation of new technologies. As a result of these technology developments, CGEn will be able to provide important new genomic services to Canadian and international researchers.

The Centre for Biodiversity Genomics (CBG) at the University of Guelph holds global leadership in the development and application of species identification systems based on sequence diversity in short, standardized gene regions (DNA barcodes). Termed DNA barcoding, this approach is hugely advancing both our knowledge of the species that share our planet and our capacity to track shifts in their abundance and distribution.

The CBG delivers two key analytical services (informatics, sequencing) to the biodiversity science community; it analyzes millions of specimens and tens of thousands of samples each year by coupling large sequencers with mainframe computers. The award from Genome Canada’s Technology Program will allow the CBG’s Innovation Unit to expand its efforts to develop the laboratory protocols and informatics systems required to capitalize on the capabilities enabled by the thumb-sized DNA sequencers developed by Oxford Nanopore Technologies.

Aside from their speed in delivering data, the low cost of these sequencers and their associated flow cells make them ideal for two purposes – accelerating the development of methods for subsequent implementation in the CBG core facility and making it possible to establish a distributed network of sequencing facilities so nations around the world can track their biodiversity. Because the CBG coordinates the research programs undertaken by the International Barcode of Life Consortium, the advances made by the Innovation Unit in the application of nanopore technology are sure to see rapid uptake on a global scale.

The Centre for Applied Genomics (TCAG), founded in 1998, has been a Genome Canada Science and Technology Platform since 2001. TCAG provides genomics support and analysis to more than 800 Principal Investigator labs per year, a total of more than 2,000 over its lifetime, spanning 45 countries, 317 academic institutions, 150 companies and 46 government agencies and non-governmental organizations. Through its work, TCAG has catalyzed many significant scientific advances. TCAG developed and hosts the Database of Genomic Variants and the Ontario Population Genomics Platform repository, leads the “MSSNG” autism genome sequencing project and the Canadian Personal Genome Project, and is the Toronto node of Canada’s Genomics Enterprise (CGEn), a national network of whole genome sequencing centres.

With additional funding from Genome Canada, TCAG will continue to actively develop novel methodologies for whole genome sequencing, genome assembly and statistical analysis of genome-wide data. These activities will complement the development and implementation of additional pipelines and methods for generating and analyzing genomic data. TCAG will continue to work with national and international partners to advance the utilization of genomics to address many facets of multidisciplinary science, including a strong focus on human diseases and neurodevelopmental disorders.