Canada takes its first leap to empower precision medicine and genomic research with the launch of the Canadian Genomics Cloud (genomicscloud.ca) software platform. Combining a national consortium of industry and academic collaborators, this public cloud computing platform is the first of its kind here in Canada, and promises to give every scientist in the country unencumbered access to award-winning technology in an altruistic manner to further Canadian research and ultimately, provide medicines and cures for those who need them.
The Canadian Genomics Cloud delivers key functionalities for genome science on the cloud, a computing paradigm that uses storage and processing resources of remote data centres that can be accessed securely over the internet. Cloud computing frees its users of substantial costs, inefficiencies, and burdens associated with maintaining hard infrastructure on-premises while providing on-demand access to massive compute capacity and a wide range of managed services.
“Exponential growth in genome sequencing is generating unprecedented volumes of data that demand cloud computing to manage and mine,” says Marc Fiume, CEO of Toronto-based DNAstack, whose team led the development of the platform to align with global standards it helped write as part of a large worldwide consortium called the Global Alliance for Genomics and Health (GA4GH). “With this launch, we are ushering into Canada the latest technologies and standards to catalyze research and service faster than ever before.”
The Canadian Genomics Cloud provides on-demand access to popular data analysis workflows like the Broad Institute’s GATK4, Verily’s Deep Variant, and Sentieon’s DNAseq. It supports machine learning through Google’s TensorFlow and secure data sharing through GA4GH Beacon and Matchmaker.
The Canadian Genomics Cloud is being developed to support CGEn, a Canadian national network of genome sequencing centres in Montreal, Toronto, and Vancouver. “We are performing whole genome sequencing on thousands of research samples across Canada and our needs to manage this big data for the community grow every day,” says Dr. Stephen Scherer, a leader of CGEn and senior scientist at The Hospital for Sick Children, and Professor of Medicine at the University of Toronto.
Scherer also recently published the Personal Genomes Project Canada, a comprehensive online public data resource that combines participants’ genome sequencing data with their health information. Marc Fiume and his co-founder of DNAstack both have their genomes listed in this database as an attempt to decrease the unease of publicly airing one’s genome.
The platform will also be used to support SickKids Cancer Sequencing (KiCS, kicsprogram.com), a pediatric cancer genome sequencing program led by Drs. Adam Shlien and David Malkin, from The Hospital for Sick Children. “Early cancer events mark the genome with unique mutational fingerprints that can give clues to a clinical treatment plan once identified. The Canadian Genomics Cloud provides the computing capacity needed for us to train machine learning models to extract signatures from genome sequence data from tumours of children with cancer.”
The Canadian Genomics Cloud is designed to support national initiatives, which call for the co-ordinated sequencing, sharing, and analysis of genomes collected from tens of thousands of individuals from across the country.
“Sharing of genomic and health-related data for biomedical research is of key importance to ensure continued progress in our understanding of human health and wellbeing,” says Dr. Bartha Knoppers, health-policy expert at McGill University and director of CGP.
The Canadian Genomics Cloud lays the foundation for an ecosystem of technical integrations that will allow data to flow securely and efficiently between systems, breaking through traditional data silos and helping to maximize the value of genomics and health data collected institutionally, regionally, and across the country. The Canadian Genomics Cloud is deployed on Google’s new cloud computing facility in Montreal, which opened earlier this month, and will soon allow federated sharing and analysis of data between multiple cloud providers including Microsoft Azure and Canada’s leading clinical record vendor.