. 2023 May 2;24(1):26.

doi: 10.1186/s12863-023-01128-3.

HostSeq: a Canadian whole genome sequencing and clinical data resource

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.

PMID: 37131148
PMCID: PMC10152008
DOI: 10.1186/s12863-023-01128-3

HostSeq: a Canadian whole genome sequencing and clinical data resource

S Yoo et al. BMC Genom Data. 2023.

. 2023 May 2;24(1):26.

doi: 10.1186/s12863-023-01128-3.

Authors

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.

PMID: 37131148
PMCID: PMC10152008
DOI: 10.1186/s12863-023-01128-3

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

**Fig. 1**
Sample and data flow in HostSeq (Aspects of graphics acquired from Wikimedia Commons)

**Fig. 2**
PCA projection of HostSeq genomes against reference superpopulations. HostSeq genomes were merged with the 1000 Genomes reference set. The first two principal components of this merged data are shown here with HostSeq genomes in black and 1000 Genomes samples colored by their superpopulation: AFR = African, AMR = Admixed American, EAS = East Asian, SAS = South Asian, EUR = European

See this image and copyright information in PMC

References

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HostSeq: a Canadian whole genome sequencing and clinical data resource

Affiliations

HostSeq: a Canadian whole genome sequencing and clinical data resource

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous