HostSeq: a Canadian whole genome sequencing and clinical data resource.

Yoo, S; Garg, E; Elliott, LT; Hung, RJ; Halevy, AR; Brooks, JD; Bull, SB; Gagnon, F; Greenwood, C; Lawless, JF; Paterson, AD; Sun, L; Zawati, MH; Lerner-Ellis, J; Abraham, R; Birol, I; Bourque, G; Garant, J-M; Gosselin, C; Li, J; Whitney, J; Thiruvahindrapuram, B; Herbrick, J-A; Lorenti, M; Reuter, MS; Adeoye, OO; Liu, S; Allen, U; Bernier, FP; Biggs, CM; Cheung, AM; Cowan, J; Herridge, M; Maslove, DM; Modi, BP; Mooser, V; Morris, SK; Ostrowski, M; Parekh, RS; Pfeffer, G; Suchowersky, O; Taher, J; Upton, J; Warren, RL; Yeung, R; Aziz, N; Turvey, SE; Knoppers, BM; Lathrop, M; Jones, S; Scherer, SW; Strug, LJ

HostSeq: a Canadian whole genome sequencing and clinical data resource.

Yoo, S Garg, E Elliott, LT Hung, RJ Halevy, AR Brooks, JD Bull, SB Gagnon, F Greenwood, C Lawless, JF Paterson, AD Sun, L Zawati, MH Lerner-Ellis, J Abraham, R Birol, I Bourque, G Garant, J-M Gosselin, C Li, J Whitney, J Thiruvahindrapuram, B Herbrick, J-A Lorenti, M Reuter, MS Adeoye, OO Liu, S Allen, U Bernier, FP Biggs, CM Cheung, AM Cowan, J Herridge, M Maslove, DM Modi, BP Mooser, V Morris, SK Ostrowski, M

Parekh, RS Pfeffer, G Suchowersky, O Taher, J Upton, J Warren, RL Yeung, R Aziz, N Turvey, SE Knoppers, BM Lathrop, M Jones, S Scherer, SW Strug, LJ

Permalink

Publisher:: BMC
Publication Type:: Journal Article
Citation:: BMC Genom Data, 2023, 24, (1), pp. 26
Issue Date:: 2023-05-02

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Published versionAdobe PDF (1.52 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Yoo, S
dc.contributor.author	Garg, E
dc.contributor.author	Elliott, LT
dc.contributor.author	Hung, RJ
dc.contributor.author	Halevy, AR
dc.contributor.author	Brooks, JD
dc.contributor.author	Bull, SB
dc.contributor.author	Gagnon, F
dc.contributor.author	Greenwood, C
dc.contributor.author	Lawless, JF
dc.contributor.author	Paterson, AD
dc.contributor.author	Sun, L
dc.contributor.author	Zawati, MH
dc.contributor.author	Lerner-Ellis, J
dc.contributor.author	Abraham, R
dc.contributor.author	Birol, I
dc.contributor.author	Bourque, G
dc.contributor.author	Garant, J-M
dc.contributor.author	Gosselin, C
dc.contributor.author	Li, J
dc.contributor.author	Whitney, J
dc.contributor.author	Thiruvahindrapuram, B
dc.contributor.author	Herbrick, J-A
dc.contributor.author	Lorenti, M
dc.contributor.author	Reuter, MS
dc.contributor.author	Adeoye, OO
dc.contributor.author	Liu, S
dc.contributor.author	Allen, U
dc.contributor.author	Bernier, FP
dc.contributor.author	Biggs, CM
dc.contributor.author	Cheung, AM
dc.contributor.author	Cowan, J
dc.contributor.author	Herridge, M
dc.contributor.author	Maslove, DM
dc.contributor.author	Modi, BP
dc.contributor.author	Mooser, V
dc.contributor.author	Morris, SK
dc.contributor.author	Ostrowski, M https://orcid.org/0000-0002-4357-3023
dc.contributor.author	Parekh, RS
dc.contributor.author	Pfeffer, G
dc.contributor.author	Suchowersky, O
dc.contributor.author	Taher, J
dc.contributor.author	Upton, J
dc.contributor.author	Warren, RL
dc.contributor.author	Yeung, R
dc.contributor.author	Aziz, N
dc.contributor.author	Turvey, SE
dc.contributor.author	Knoppers, BM
dc.contributor.author	Lathrop, M
dc.contributor.author	Jones, S
dc.contributor.author	Scherer, SW
dc.contributor.author	Strug, LJ
dc.date.accessioned	2024-03-19T04:12:48Z
dc.date.available	2023-02-22
dc.date.available	2024-03-19T04:12:48Z
dc.date.issued	2023-05-02
dc.identifier.citation	BMC Genom Data, 2023, 24, (1), pp. 26
dc.identifier.issn	2730-6844
dc.identifier.issn	2730-6844
dc.identifier.uri	http://hdl.handle.net/10453/176914
dc.description.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.
dc.format	Electronic
dc.language	eng
dc.publisher	BMC
dc.relation.ispartof	BMC Genom Data
dc.relation.isbasedon	10.1186/s12863-023-01128-3
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.mesh	Humans
dc.subject.mesh	SARS-CoV-2
dc.subject.mesh	COVID-19
dc.subject.mesh	Canada
dc.subject.mesh	Genomics
dc.subject.mesh	Whole Genome Sequencing
dc.subject.mesh	Humans
dc.subject.mesh	Genomics
dc.subject.mesh	Canada
dc.subject.mesh	Whole Genome Sequencing
dc.subject.mesh	COVID-19
dc.subject.mesh	SARS-CoV-2
dc.subject.mesh	Humans
dc.subject.mesh	SARS-CoV-2
dc.subject.mesh	COVID-19
dc.subject.mesh	Canada
dc.subject.mesh	Genomics
dc.subject.mesh	Whole Genome Sequencing
dc.title	HostSeq: a Canadian whole genome sequencing and clinical data resource.
dc.type	Journal Article
utslib.citation.volume	24
utslib.location.activity	England
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Science
utslib.copyright.status	open_access	*
dc.date.updated	2024-03-19T04:12:46Z
pubs.issue	1
pubs.publication-status	Published online
pubs.volume	24
utslib.citation.issue	1

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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/176914