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

doi:10.1016/j.xgen.2021.100033

CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis

Cell Genom. 2021 Nov 10;1(2):100033. doi: 10.1016/j.xgen.2021.100033.

Authors

L Jonathan Dursi¹, Zoltan Bozoky², Richard de Borja^{3

4}, Haoyuan Li⁵, David Bujold⁶, Adam Lipski^{5

7}, Shaikh Farhan Rashid¹, Amanjeev Sethi¹, Neelam Memon⁵, Dashaylan Naidoo⁵, Felipe Coral-Sasso⁵, Matthew Wong⁸, P-O Quirion⁶, Zhibin Lu⁹, Samarth Agarwal¹⁰, Yuriy Pavlov¹, Andrew Ponomarev^{5

11}, Mia Husic¹², Krista Pace¹, Samantha Palmer¹, Stephanie A Grover¹³, Sevan Hakgor⁴, Lillian L Siu⁴, David Malkin¹⁴, Carl Virtanen⁹, Trevor J Pugh^{3

4

15}, Pierre-Étienne Jacques¹⁶, Yann Joly^{17

18}, Steven J M Jones^{5

19}, Guillaume Bourque^{18

20

21}, Michael Brudno^{1

22

23}

Affiliations

¹ DATA Team, University Health Network, Toronto, ON, M5G 2C4, Canada.
² Providence Health Care, Vancouver, BC, V6Z 1Y6, Canada.
³ Ontario Institute of Cancer Research, Toronto, ON, M5G 0A3, Canada.
⁴ Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada.
⁵ Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, V5Z 4S6, Canada.
⁶ Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada.
⁷ Zymeworks, Vancouver, BC, V6H 3V9, Canada.
⁸ University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
⁹ University Health Network, Toronto, ON, M5G 2C4, Canada.
¹⁰ University of Toronto, Toronto, ON, M5T 3A1, Canada.
¹¹ GenX, Nottingham, NG1 1GF, UK.
¹² Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
¹³ Genetics and Genome Biology Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, M5G 1X8, Canada.
¹⁴ Division of Haematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, M5G 1X8, Canada.
¹⁵ Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
¹⁶ Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
¹⁷ Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.
¹⁸ Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.
¹⁹ Department of Medical Genetics, University of British Columbia, BC, V6H 3N1, Canada.
²⁰ Canadian Center for Computational Genomics (C3G), McGill University, Montreal, QC, H3A 0G1, Canada.
²¹ McGill Genome Center, Faculty of Medicine, McGill University, Montreal, QC, H3A 0G1, Canada.
²² Department of Computer Science, University of Toronto, Toronto, ON, M5T 3A1, Canada.
²³ Vector Institute, Toronto, ON, M5G 1M1, Canada.

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.

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News