HostSeq: a Canadian whole genome sequencing and clinical data resource

S Yoo; E Garg; L T Elliott; R J Hung; A R Halevy; J D Brooks; S B Bull; F Gagnon; Cmt Greenwood; J F Lawless; A D Paterson; L Sun; M H Zawati; J Lerner-Ellis; Rjs Abraham; I Birol; G Bourque; J-M Garant; C Gosselin; J Li; J Whitney; B Thiruvahindrapuram; J-A Herbrick; M Lorenti; M S Reuter; O O Adeoye; S Liu; U Allen; F P Bernier; C M Biggs; A M Cheung; J Cowan; M Herridge; D M Maslove; B P Modi; V Mooser; S K Morris; M Ostrowski; R S Parekh; G Pfeffer; O Suchowersky; J Taher; J Upton; R L Warren; Rsm Yeung; N Aziz; S E Turvey; B M Knoppers; M Lathrop; Sjm Jones; S W Scherer; L J Strug

doi:10.1186/s12863-023-01128-3

HostSeq: a Canadian whole genome sequencing and clinical data resource

BMC Genom Data. 2023 May 2;24(1):26. doi: 10.1186/s12863-023-01128-3.

Authors

S Yoo^#^{1

2}, E Garg^#³, L T Elliott³, R J Hung^{4

5}, A R Halevy¹, J D Brooks⁴, S B Bull^{4

5}, F Gagnon⁴, Cmt Greenwood^{6

7}, J F Lawless⁸, A D Paterson^{1

4}, L Sun⁴, M H Zawati⁶, J Lerner-Ellis^{4

9}, Rjs Abraham¹⁰, I Birol¹⁰, G Bourque⁶, J-M Garant¹⁰, C Gosselin¹⁰, J Li¹⁰, J Whitney¹, B Thiruvahindrapuram¹, J-A Herbrick¹, M Lorenti¹, M S Reuter¹, O O Adeoye¹, S Liu¹, U Allen^{1

4}, F P Bernier^{11

12}, C M Biggs^{13

14

15}, A M Cheung¹⁶, J Cowan^{2

17}, M Herridge¹⁶, D M Maslove¹⁸, B P Modi¹⁴, V Mooser⁶, S K Morris^{1

4}, M Ostrowski^{4

19}, R S Parekh^{1

4

20}, G Pfeffer¹¹, O Suchowersky²¹, J Taher^{4

9}, J Upton^{1

4}, R L Warren¹⁰, Rsm Yeung^{1

4}, N Aziz¹, S E Turvey^{13

14}, B M Knoppers⁶, M Lathrop⁶, Sjm Jones¹⁰, S W Scherer^{1

4}, L J Strug^{22

23}

Affiliations

¹ The Hospital for Sick Children, Toronto, ON, Canada.
² University of Ottawa, Ottawa, ON, Canada.
³ Simon Fraser University, Burnaby, BC, Canada.
⁴ University of Toronto, Toronto, ON, Canada.
⁵ Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
⁶ McGill University, Montreal, QC, Canada.
⁷ Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
⁸ University of Waterloo, Waterloo, ON, Canada.
⁹ Sinai Health System, Toronto, ON, Canada.
¹⁰ Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
¹¹ University of Calgary, Calgary, AB, Canada.
¹² Alberta Children's Hospital, Calgary, AB, Canada.
¹³ University of British Columbia, Vancouver, BC, Canada.
¹⁴ BC Children's Hospital, Vancouver, BC, Canada.
¹⁵ St. Paul's Hospital, Vancouver, BC, Canada.
¹⁶ University Health Network, Toronto, ON, Canada.
¹⁷ The Ottawa Hospital Research Institute, Ottawa, ON, Canada.
¹⁸ Queen's University, Kingston, ON, Canada.
¹⁹ St. Michael's Hospital, Unity Health, Toronto, ON, Canada.
²⁰ Women's College Hospital, Toronto, ON, Canada.
²¹ University of Alberta, Edmonton, AB, Canada.
²² The Hospital for Sick Children, Toronto, ON, Canada. lisa.strug@utoronto.ca.
²³ University of Toronto, Toronto, ON, Canada. lisa.strug@utoronto.ca.

^# Contributed equally.

Abstract

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

Keywords: COVID-19; Clinical databank; Host genetics; SARS-CoV-2; Whole genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Canada / epidemiology
Genomics
Humans
SARS-CoV-2* / genetics
Whole Genome Sequencing

Abstract

Publication types

MeSH terms

Grants and funding