Cell Genomics (Nov 2021)
CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis
- L. Jonathan Dursi,
- Zoltan Bozoky,
- Richard de Borja,
- Haoyuan Li,
- David Bujold,
- Adam Lipski,
- Shaikh Farhan Rashid,
- Amanjeev Sethi,
- Neelam Memon,
- Dashaylan Naidoo,
- Felipe Coral-Sasso,
- Matthew Wong,
- P-O Quirion,
- Zhibin Lu,
- Samarth Agarwal,
- Yuriy Pavlov,
- Andrew Ponomarev,
- Mia Husic,
- Krista Pace,
- Samantha Palmer,
- Stephanie A. Grover,
- Sevan Hakgor,
- Lillian L. Siu,
- David Malkin,
- Carl Virtanen,
- Trevor J. Pugh,
- Pierre-Étienne Jacques,
- Yann Joly,
- Steven J.M. Jones,
- Guillaume Bourque,
- Michael Brudno
Affiliations
- L. Jonathan Dursi
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada; Corresponding author
- Zoltan Bozoky
- Providence Health Care, Vancouver, BC, V6Z 1Y6, Canada
- Richard de Borja
- Ontario Institute of Cancer Research, Toronto, ON, M5G 0A3, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
- Haoyuan Li
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada
- David Bujold
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
- Adam Lipski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada; Zymeworks, Vancouver, BC, V6H 3V9, Canada
- Shaikh Farhan Rashid
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada
- Amanjeev Sethi
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada
- Neelam Memon
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada
- Dashaylan Naidoo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada
- Felipe Coral-Sasso
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada
- Matthew Wong
- University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- P-O Quirion
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
- Zhibin Lu
- University Health Network, Toronto, ON, M5G 2C4, Canada
- Samarth Agarwal
- University of Toronto, Toronto, ON, M5T 3A1, Canada
- Yuriy Pavlov
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada
- Andrew Ponomarev
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada; GenX, Nottingham, NG1 1GF, UK
- Mia Husic
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Krista Pace
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada
- Samantha Palmer
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada
- Stephanie A. Grover
- Genetics and Genome Biology Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, M5G 1X8, Canada
- Sevan Hakgor
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
- Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
- David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, M5G 1X8, Canada
- Carl Virtanen
- University Health Network, Toronto, ON, M5G 2C4, Canada
- Trevor J. Pugh
- Ontario Institute of Cancer Research, Toronto, ON, M5G 0A3, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Pierre-Étienne Jacques
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
- Yann Joly
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada; Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada; Department of Medical Genetics, University of British Columbia, BC, V6H 3N1, Canada
- Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada; Canadian Center for Computational Genomics (C3G), McGill University, Montreal, QC, H3A 0G1, Canada; McGill Genome Center, Faculty of Medicine, McGill University, Montreal, QC, H3A 0G1, Canada
- Michael Brudno
- DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada; Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada; Vector Institute, Toronto, ON, M5G 1M1, Canada; Corresponding author
- Journal volume & issue
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Vol. 1,
no. 2
p. 100033
Abstract
We present the Canadian Distributed Infrastructure for Genomics (CanDIG) platform, which enables federated querying and analysis of human genomics and linked biomedical data. CanDIG leverages the standards and frameworks of the Global Alliance for Genomics and Health (GA4GH) and currently hosts data for five pan-Canadian projects. We describe CanDIG’s key design decisions and features as a guide for other federated data systems.
