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HostSeq: a Canadian whole genome sequencing and clinical data resource.
Yoo, S; Garg, E; Elliott, L T; Hung, R J; Halevy, A R; Brooks, J D; Bull, S B; Gagnon, F; Greenwood, Cmt; Lawless, J F; Paterson, A D; Sun, L; Zawati, M H; Lerner-Ellis, J; Abraham, Rjs; Birol, I; Bourque, G; Garant, J-M; Gosselin, C; Li, J; Whitney, J; Thiruvahindrapuram, B; Herbrick, J-A; Lorenti, M; Reuter, M S; Adeoye, O O; Liu, S; Allen, U; Bernier, F P; Biggs, C M; Cheung, A M; Cowan, J; Herridge, M; Maslove, D M; Modi, B P; Mooser, V; Morris, S K; Ostrowski, M; Parekh, R S; Pfeffer, G; Suchowersky, O; Taher, J; Upton, J; Warren, R L; Yeung, Rsm; Aziz, N; Turvey, S E; Knoppers, B M; Lathrop, M; Jones, Sjm.
  • Yoo S; The Hospital for Sick Children, Toronto, ON, Canada.
  • Garg E; University of Ottawa, Ottawa, ON, Canada.
  • Elliott LT; Simon Fraser University, Burnaby, BC, Canada.
  • Hung RJ; Simon Fraser University, Burnaby, BC, Canada.
  • Halevy AR; University of Toronto, Toronto, ON, Canada.
  • Brooks JD; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
  • Bull SB; The Hospital for Sick Children, Toronto, ON, Canada.
  • Gagnon F; University of Toronto, Toronto, ON, Canada.
  • Greenwood C; University of Toronto, Toronto, ON, Canada.
  • Lawless JF; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
  • Paterson AD; University of Toronto, Toronto, ON, Canada.
  • Sun L; McGill University, Montreal, QC, Canada.
  • Zawati MH; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
  • Lerner-Ellis J; University of Waterloo, Waterloo, ON, Canada.
  • Abraham R; The Hospital for Sick Children, Toronto, ON, Canada.
  • Birol I; University of Toronto, Toronto, ON, Canada.
  • Bourque G; University of Toronto, Toronto, ON, Canada.
  • Garant JM; McGill University, Montreal, QC, Canada.
  • Gosselin C; University of Toronto, Toronto, ON, Canada.
  • Li J; Sinai Health System, Toronto, ON, Canada.
  • Whitney J; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
  • Thiruvahindrapuram B; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
  • Herbrick JA; McGill University, Montreal, QC, Canada.
  • Lorenti M; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
  • Reuter MS; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
  • Adeoye OO; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
  • Liu S; The Hospital for Sick Children, Toronto, ON, Canada.
  • Allen U; The Hospital for Sick Children, Toronto, ON, Canada.
  • Bernier FP; The Hospital for Sick Children, Toronto, ON, Canada.
  • Biggs CM; The Hospital for Sick Children, Toronto, ON, Canada.
  • Cheung AM; The Hospital for Sick Children, Toronto, ON, Canada.
  • Cowan J; The Hospital for Sick Children, Toronto, ON, Canada.
  • Herridge M; The Hospital for Sick Children, Toronto, ON, Canada.
  • Maslove DM; The Hospital for Sick Children, Toronto, ON, Canada.
  • Modi BP; University of Toronto, Toronto, ON, Canada.
  • Mooser V; University of Calgary, Calgary, AB, Canada.
  • Morris SK; Alberta Children's Hospital, Calgary, AB, Canada.
  • Ostrowski M; University of British Columbia, Vancouver, BC, Canada.
  • Parekh RS; BC Children's Hospital, Vancouver, BC, Canada.
  • Pfeffer G; St. Paul's Hospital, Vancouver, BC, Canada.
  • Suchowersky O; University Health Network, Toronto, ON, Canada.
  • Taher J; University of Ottawa, Ottawa, ON, Canada.
  • Upton J; The Ottawa Hospital Research Institute, Ottawa, ON, Canada.
  • Warren RL; University Health Network, Toronto, ON, Canada.
  • Yeung R; Queen's University, Kingston, ON, Canada.
  • Aziz N; BC Children's Hospital, Vancouver, BC, Canada.
  • Turvey SE; McGill University, Montreal, QC, Canada.
  • Knoppers BM; The Hospital for Sick Children, Toronto, ON, Canada.
  • Lathrop M; University of Toronto, Toronto, ON, Canada.
  • Jones S; University of Toronto, Toronto, ON, Canada.
BMC Genom Data ; 24(1): 26, 2023 05 02.
Article in English | MEDLINE | ID: covidwho-2320700
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: North America Language: English Journal: BMC Genom Data Year: 2023 Document Type: Article Affiliation country: S12863-023-01128-3

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: North America Language: English Journal: BMC Genom Data Year: 2023 Document Type: Article Affiliation country: S12863-023-01128-3