elliottlab.ca

A Canadian whole-genome sequencing and clinical data resource—HostSeq. Launched in April 2020 as part of a national collaboration among 13 independent epidemiological SARS‑CoV‑2 studies across five Canadian provinces, HostSeq is a database of clinical information and whole genome sequencing data from 10,000 SARS-CoV-2-infected Canadians, aimed at supporting research communities in understanding the associated health impacts and developing intervention measures, including vaccines. Individual‑level data are accessible to researchers with approved data access and compliance agreement. HostSeq’s methodology—including aggregation and sampling mechanisms—is published in BMC Genomic Data (Yoo & Garg 2023).

HostSeq was funded by Canada’s national platform for genome sequencing and analysis (CGEn), which is supported by the Canada Foundation for Innovation (CFI) through its Major Science Initiatives Fund (MSIF). CGEn operates as an integrated national platform with sequencing nodes based in Toronto (The Centre for Applied Genomics at The Hospital for Sick Children), Montréal (McGill Genome Centre at McGill University), and Vancouver (Canada’s Michael Smith Genome Sciences Centre at BC Cancer). The epidemiological studies contributing to HostSeq were funded through institutional, provincial, and federal research grants, as described in Yoo & Garg 2023.

L.T. Elliott, E. Garg (Simon Fraser University); L.J. Strug, S. Yoo, A.R. Halevy, J. Whitney, B. Thiruvahindrapuram, J.‑A. Herbrick, M. Lorenti, M.S. Reuter, O.O. Adeoye, S. Liu, U. Allen, S.K. Morris, R.S. Parekh, N. Aziz, S.W. Scherer (The Hospital for Sick Children); R.J. Hung, J.D. Brooks, S.B. Bull, F. Gagnon, A.D. Paterson, L. Sun, M. Ostrowski (University of Toronto); C.M.T. Greenwood, M.H. Zawati, G. Bourque, V. Mooser, B.M. Knoppers, M. Lathrop (McGill University); J.F. Lawless (University of Waterloo); J. Lerner‑Ellis, J. Taher (Sinai Health System); R.J.S. Abraham, I. Birol, J.‑M. Garant, C. Gosselin, J. Li, R.L. Warren, S.J.M. Jones (Canada’s Michael Smith Genome Sciences Centre); F.P. Bernier, G. Pfeffer (University of Calgary); C.M. Biggs, B.P. Modi, S.E. Turvey (University of British Columbia); A.M. Cheung, M. Herridge (University Health Network); J. Cowan (University of Ottawa); D.M. Maslove (Queen’s University); O. Suchowersky (University of Alberta); M. Ostrowski (St. Michael’s Hospital) contributed to the creation and preprocessing of these data.

Oxford Brain Imaging Genetics Server—BIG40. This open data server contains results from GWAS of almost 4,000 imaging-derived phenotypes from the multimodal brain imaging in UK Biobank, using data from the 40,000 subject imaging data release from early 2020. The discovery sample size was 22,138 and the replication sample was 11,086. Chromosomes 1:22 and X are included, resulting in association tests with 20,381,044 genetic variants.

The work was funded by the Wellcome Trust. Compute resources were provided by the Oxford Biomedical Research Computing (BMRC) facility (a joint development between Oxford's Wellcome Centre for Human Genetics and the Big Data Institute, supported by Health Data Research UK and the NIHR Oxford Biomedical Research Centre). This work was conducted in part using the UK Biobank Resource under Application Number 8107.

L.T. Elliott, W. Chen (Simon Fraser University); S.M. Smith, G. Douaud, F. Alfaro-Almagro, P. McCarthy, D. Mortimer, S. Shi (University of Oxford); K. Sharp (Genomics PLC) contributed to the creation and analysis of these data.

elliottlab

Data