Founded in 1998 by Canadian genomics pioneers Drs. Lap-Chee Tsui and Stephen Scherer, The Centre for Applied Genomics (TCAG) provides world-leading infrastructure, technical expertise, and experimental and informatics support for innovative research in genomics. TCAG is located on a full floor of the Research Institute of The Hospital for Sick Children (SickKids), in the Peter Gilgan Centre for Research and Learning in downtown Toronto, and is affiliated with the McLaughlin Centre and the University of Toronto. The centre is a founding member of Canada’s Genomics Enterprise (CGEn), a national genomics platform that is one of the Major Science Initiatives funded by the Canada Foundation for Innovation (CFI) as a national platform critical to Canada’s research success. Its friendly staff of approximately 100 includes highly skilled bioinformatics, statistics, and laboratory personnel, core facility managers, embedded researchers, Associate Investigators, and an administrative team. The group works closely with client scientists to ensure success of their projects.
TCAG contains individual core facilities that collectively form a full-service, end-to-end genomics pipeline that can accommodate projects from the very small to the very large. These include cores in Informatics & Biostatistics, Sequencing, Microarrays & Genotyping, and Cytogenomics & Biobanking. The facilities are run by highly experienced managers (with an average of 8 years in the role), who consult with TCAG clients to ensure optimum experimental approaches. Data are generated on a fee-for-service, cost-recovery basis, and belong to the client. TCAG data handling and analysis activities take advantage of the SickKids High Performance Computing Facility (HPF) and HPC4Health Compute Canada node, both housed in our PGCRL building, as well as cloud-based resources. The centre also developed and hosts the Database of Genomic Variants (DGV). Last year, the DGV website was visited over 230,000 times by users from 88 different countries and is cited in over 350 publications every year.
Importantly, TCAG supports projects across a wide variety of disciplines: not only human biomedical research, but also in areas as diverse as agriculture and agri-food, fisheries and oceans, biopharma research, translational diagnostics, public health, bioinformatics, biostatistics, environmental sciences and biodiversity, and many other disciplines. Work for client projects is acknowledged in hundreds of publications per year, from the over 800 Principal Investigator scientists using TCAG’s services annually.
There have been many milestones in TCAG’s long history, some of which are highlighted below:
- Since 2006, TCAG has provided services to over 2,200 laboratories: 85% from Canada including all ten Canadian Provinces; 45 countries; 331 academic institutions (universities, teaching hospitals and colleges); 157 companies (58% Canadian), and 49 government or NGO institutions. Dozens of trainees (students, fellows, visiting scientists, clinician-scientists, etc.) have trained within the facility.
- TCAG is the first genome centre in Canada to install and operate Illumina HiSeq X whole genome sequencers; these are run alongside Illumina NovaSeq and other HiSeq instruments, and many other technologies including those for single-cell genomics (10X Genomics Chromium), single-molecule, long-read nanopore sequencing (PacBio Sequel), sensitive quantitative detection methodologies (digital droplet PCR, qPCR), and an extensive slate of targeted genotyping (Agena, Taqman, etc.) and genomic analysis resources.
- TCAG developed the Ontario Population Genomics Platform repository that contains over 2,500 cell lines, DNA and demographic data from healthy controls, and has comprehensively genotyped over 850 of these. These data and population control DNA samples are available as a public resource.
- Under the leadership of current Director Stephen Scherer, and in collaboration with Google, Verily, BioTeam and DNAstack, TCAG leads the Autism Speaks “MSSNG” project, generating whole genome sequences from 10,000 members of families with autistic children. Over 8,000 genomes have been completed to date, with analysis of the first 5,200 reported in Nature Neuroscience. The capacity and capabilities built for MSSNG have resulted in many benefits to TCAG clients. One recent example is the development of an improved pipeline for whole-genome copy number variation analysis.
- TCAG has leveraged a total of over $223 million in funding over the past 20 years, including over $93 million in billed, cost-recovery services contributing to research studies in Canada and around the world. Major funding partners include CFI, the Ontario government’s Ministry of Research, Innovation and Science, Genome Canada, CIHR, the SickKids Foundation, and the McLaughlin Centre of the Unversity of Toronto.
Our group at The Centre for Applied Genomics will be pleased to help you with your research. Contacts for specific TCAG facilities can be found on our website. For general inquiries, please get in touch with TCAG’s Manager, Jo-Anne Herbrick, at (416) 813-8140, or jherbrick@sickkids.ca.
