Canadian Genomics Enterprise (Canadian Foundation for Innovation)

The Canadian Genomics Enterprise (CGEn) is a partnership that links the three nationally funded genome centres in Montreal (McGill University Centre for Molecular and Computational Genomics), Toronto (The Centre for Applied Genomics at Torontoʼs Hospital for Sick Children) and Vancouver (Canadaʼs Michael Smith Genome Science Centre at the BC Cancer Agency) to enhance the national capacity for sequencing and informatics analysis. CGEn was recently awarded $58M of infrastructure funding from the Canadian Foundation for Innovation.

Genome Innovation Network (GIN)
The Centre is responsible for two Genome Canada Genome Innovation Network (GIN) nodes:

McGill University and Genome Québec Innovation Centre (MUQGIC)
Through its Genome Canada GIN node – MUQGIC - the Centre applies its internal scientific and technological expertise Canadian researchers access to accurate, cost efficient genomics using the best available technologies and analysis methodologies. The GIN node supports Genome Canada and other large-scale genomics projects with state-of-the-art approaches. Principal focuses are methodologies for genetic of common (complex) and Mendelian disease traits - ranging from GWAS to whole-exome/whole-genome sequencing and beyond (e.g. single-cell disease genomics, genome-editing) – and the development of innovative population-based epigenomic tools to understand the aetiological basis of human disease.

Canadian Center for Computational Genomics
The Canadian Center for Computational Genomics (C3G) is a collaborative platform for bioinformatics and computational genomics led by Guillaume Bourque at MUGQIC and Michael Brudno at the High Performance Computing for Health (HPC4Health) centre in Toronto. C3G provides advanced analysis tools and high performance computing resources to analyze genomics data for a broad research community. This resource enables health researchers, and more broadly life scientists, to explore their data sets in unprecedented ways.

Centre of Genomics and Policy

The Centre for Genomics and Policy (CGP) works at the crossroads of law, medicine, and public policy. Applying a multidisciplinary perspective and collaborating with national and international partners, the CGP analyzes the socio-ethical and legal norms influencing the promotion, prevention and protection of human health.

McGill Epigenome Mapping & Data Coordination Centres

The McGill Epigenome Mapping and Data Coordination Centres were established in 2012 under the CIHR/CEEHRC Epigenetics, Environment and Health Signature Program, to support large-scale human epigenome mapping for a broad spectrum of cell types and diseases. The generation of comprehensive epigenome maps at McGill University is part of a larger international effort that is coordinated by the International Human Epigenome Consortium (IHEC), whose overall long-term objective is to determine the extent to which the epigenome shapes human populations over generations and in response to the environment. New resources for epigenome mapping are being developed for large-scale epigenome mapping studies, e.g. MethylSeq approach (PMID: 26021296).

Controlled access to data can be gained via a portal, which takes advantage of Compute Canada high-performance computing cluster resources to manage the large volume of data associated from the generation of reference epigenome maps. The portal provides the integrated datasets for the CIHR CEEHRC, EU Blueprint, NIH Roadmap, ENCODE, CREST JST and DEEP projects.

Single Cell Genomics

Single Cell Genomics give the unprecedented ability to study cell subpopulations, cancer tissue heterogeneity, and germline mosaicism, as well as regulatory cascades at the single cell level. Currently, we are applying microfluidic based technologies, and developing our own microfluidic chips, aiming to characterize single cells for transcript expression, mutations or copy number changes as well as epigenetic modifications and functional genomic approaches mentioned above. Particularly exciting is the development of approaches for whole genome sequencing of single cells. As suitable methodologies are being developed, our ability to generate low cost whole genome sequence will be critical to capitalize on these developments and characterize genomes from thousands of single cells derived from cancer patients. Intensive development work of such methodologies is ongoing in close collaboration with companies such as Fluidigm, Nanostring and BioRad. These developments will be further stimulated by our increase in sequencing capacity coupled with decreased costs.