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      The Biobanque québécoise de la COVID-19 (BQC19)—A cohort to prospectively study the clinical and biological determinants of COVID-19 clinical trajectories

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          Abstract

          SARS-CoV-2 infection causing the novel coronavirus disease 2019 (COVID–19) has been responsible for more than 2.8 million deaths and nearly 125 million infections worldwide as of March 2021. In March 2020, the World Health Organization determined that the COVID–19 outbreak is a global pandemic. The urgency and magnitude of this pandemic demanded immediate action and coordination between local, regional, national, and international actors. In that mission, researchers require access to high-quality biological materials and data from SARS-CoV-2 infected and uninfected patients, covering the spectrum of disease manifestations. The “Biobanque québécoise de la COVID-19” (BQC19) is a pan–provincial initiative undertaken in Québec, Canada to enable the collection, storage and sharing of samples and data related to the COVID-19 crisis. As a disease-oriented biobank based on high-quality biosamples and clinical data of hospitalized and non-hospitalized SARS-CoV-2 PCR positive and negative individuals. The BQC19 follows a legal and ethical management framework approved by local health authorities. The biosamples include plasma, serum, peripheral blood mononuclear cells and DNA and RNA isolated from whole blood. In addition to the clinical variables, BQC19 will provide in-depth analytical data derived from the biosamples including whole genome and transcriptome sequencing, proteome and metabolome analyses, multiplex measurements of key circulating markers as well as anti-SARS-CoV-2 antibody responses. BQC19 will provide the scientific and medical communities access to data and samples to better understand, manage and ultimately limit, the impact of COVID-19. In this paper we present BQC19, describe the process according to which it is governed and organized, and address opportunities for future research collaborations. BQC19 aims to be a part of a global communal effort addressing the challenges of COVID–19.

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          A minimal common outcome measure set for COVID-19 clinical research

          Summary Clinical research is necessary for an effective response to an emerging infectious disease outbreak. However, research efforts are often hastily organised and done using various research tools, with the result that pooling data across studies is challenging. In response to the needs of the rapidly evolving COVID-19 outbreak, the Clinical Characterisation and Management Working Group of the WHO Research and Development Blueprint programme, the International Forum for Acute Care Trialists, and the International Severe Acute Respiratory and Emerging Infections Consortium have developed a minimum set of common outcome measures for studies of COVID-19. This set includes three elements: a measure of viral burden (quantitative PCR or cycle threshold), a measure of patient survival (mortality at hospital discharge or at 60 days), and a measure of patient progression through the health-care system by use of the WHO Clinical Progression Scale, which reflects patient trajectory and resource use over the course of clinical illness. We urge investigators to include these key data elements in ongoing and future studies to expedite the pooling of data during this immediate threat, and to hone a tool for future needs.
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            Human genetics: lessons from Quebec populations.

            C Scriver (2000)
            The population of Quebec, Canada (7.3 million) contains approximately 6 million French Canadians; they are the descendants of approximately 8500 permanent French settlers who colonized Nouvelle France between 1608 and 1759. Their well-documented settlements, internal migrations, and natural increase over four centuries in relative isolation (geographic, linguistic, etc.) contain important evidence of social transmission of demographic behavior that contributed to effective family size and population structure. This history is reflected in at least 22 Mendelian diseases, occurring at unusually high prevalence in its subpopulations. Immigration of non-French persons during the past 250 years has given the Quebec population further inhomogeneity, which is apparent in allelic diversity at various loci. The histories of Quebec's subpopulations are, to a great extent, the histories of their alleles. Rare pathogenic alleles with high penetrance and associated haplotypes at 10 loci (CFTR, FAH, HBB, HEXA, LDLR, LPL, PAH, PABP2, PDDR, and SACS) are expressed in probands with cystic fibrosis, tyrosinemia, beta-thalassemia, Tay-Sachs, familial hypercholesterolemia, hyperchylomicronemia, PKU, oculopharyngeal muscular dystrophy, pseudo vitamin D deficiency rickets, and spastic ataxia of Charlevoix-Saguenay, respectively) reveal the interpopulation and intrapopulation genetic diversity of Quebec. Inbreeding does not explain the clustering and prevalence of these genetic diseases; genealogical reconstructions buttressed by molecular evidence point to founder effects and genetic drift in multiple instances. Genealogical estimates of historical meioses and analysis of linkage disequilibrium show that sectors of this young population are suitable for linkage disequilibrium mapping of rare alleles. How the population benefits from what is being learned about its structure and how its uniqueness could facilitate construction of a genomic map of linkage disequilibrium are discussed.
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              The Saguenay-Lac-Saint-Jean asthma familial collection: the genetics of asthma in a young founder population.

              C Laprise (2014)
              To study the genetics of asthma, a familial collection was built in the Saguenay-Lac-Saint-Jean (SLSJ) region, which is localized in northeastern Quebec, Canada, and which is characterized by a young founder effect. Recruitment was performed through probands with a specific asthma phenotype. The collection includes 1394 individuals distributed in 271 families. A phenotypic profile including more than 75 phenotypic characteristics was defined for each participant using a standardized questionnaire, respiratory measures and allergic tests. A genome-wide association study on 1214 of these samples for asthma-related phenotypes (asthma, atopy and rhinitis) and for white blood cell types was performed. These analyses allowed associating 10 single nucleotide polymorphisms (SNPs) with P<1 × 10(-5) with asthma-related phenotypes and 11 SNPs with white blood cell counts. Among them, four SNPs are located in or near genes with functions related to asthma or allergy. Moreover, several loci were identified as 5q31.1 that includes 22 SNPs associated with atopy (P<1 × 10(-3)) and located near a cytokine cluster, and 17q21.2 with seven SNPs associated with asthma. This study highlights the value of a familial collection with a fine phenotypic description and characterized by a young founder effect in the search of the genetic determinants involved in complex traits such as asthma.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: Funding acquisitionRole: Project administrationRole: Resources
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: Resources
                Role: ConceptualizationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: Project administrationRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: Project administrationRole: Resources
                Role: ConceptualizationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: Supervision
                Role: InvestigationRole: Project administrationRole: ResourcesRole: Supervision
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: InvestigationRole: Project administrationRole: Supervision
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                19 May 2021
                2021
                19 May 2021
                : 16
                : 5
                : e0245031
                Affiliations
                [1 ] Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay–Lac-Saint-Jean, Saguenay, QC, Canada
                [2 ] Department of Pharmacology-Physiology, Medicine and Health Sciences Faculty, Université de Sherbrooke, Sherbrooke, QC, Canada
                [3 ] The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, QC, Canada
                [4 ] Department of Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
                [5 ] Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
                [6 ] McGill Genome Centre and Department of Human Genetics, McGill University, Montréal, QC, Canada
                [7 ] Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
                [8 ] Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
                [9 ] Génome Québec, Montreal, QC, Canada
                [10 ] Department of Immunity and Viral Infections, Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
                [11 ] CIUSSS du Nord-de-l’Ile-de-Montréal—Hôpital du Sacré-Cœur-de-Montréal, Montreal, QC, Canada
                [12 ] Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
                [13 ] Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
                [14 ] Centre de Recherche du Centre Hospitalier Universitaire de Québec, Regenerative Medicine Division, Québec, QC, Canada
                [15 ] Department of Surgery, Faculty of Medicine, Université Laval, Quebec, QC, Canada
                [16 ] Fonds de Recherche du Québec Santé, Montreal, QC, Canada
                [17 ] Département des Sciences Fondamentales, Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada
                [18 ] Department of Neurosciences, Université de Montréal, Montreal, QC, Canada
                [19 ] Quebec Heart and Lung Institute, Quebec, QC, Canada
                [20 ] Institut du Cancer de Montréal, Montreal, QC, Canada
                [21 ] Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
                [22 ] Département de Médecine, Service d’Infectiologie, Centre de Recherche Clinique du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
                [23 ] Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
                [24 ] Department of Epidemiology and Department of Human Genetics, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
                [25 ] Division of Respiratory Medicine, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada
                [26 ] Centre Hospitalier Universitaire de Québec–Université Laval Research Center, Population Health and Optimal Health Practices Research Unit, Trauma-Emergency-Critical Care Medicine, Québec City, QC, Canada
                [27 ] Division of Critical Care Medicine, Department of Anesthesiology and Critical Care Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
                [28 ] CIUSSS de l’Ouest-de-l’Ile-de-Montréal, Montreal, QC, Canada
                [29 ] Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
                [30 ] Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
                [31 ] Division of Medical Microbiology, Department of Laboratory Medicine, McGill University Health Centre, Montreal, QC, Canada
                [32 ] Division of Critical Care Medicine, Department of Medicine, Universite de Montreal, Montreal, QC, Canada
                [33 ] CIUSSS de l’Est-de-l’Ile-de-Montréal, Hôpital Maisonneuve-Rosemont Research Centre, Montreal, QC, Canada
                [34 ] Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
                Mater Misericordiae University Hospital, IRELAND
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                ¶ Membership of the BQC19’ contributors is listed in the Acknowledgments.

                Author information
                https://orcid.org/0000-0002-8773-575X
                https://orcid.org/0000-0002-9486-1105
                https://orcid.org/0000-0001-5675-8791
                Article
                PONE-D-20-40382
                10.1371/journal.pone.0245031
                8133500
                34010280
                5bf05d7d-5104-42ab-8deb-b8a420243a4e
                © 2021 Tremblay et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 December 2020
                : 3 April 2021
                Page count
                Figures: 6, Tables: 4, Pages: 18
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100000156, Fonds de Recherche du Québec - Santé;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100013062, Génome Québec;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100011094, Public Health Agency of Canada;
                Award Recipient :
                This biobank is financially support by the Fonds de recherche du Québec - Santé (FRQS), Genome Québec and the Public Health Agency of Canada (PHAC). The funders initiated the project to support the research community facing the COVID-19 related sanitary emergency.
                Categories
                Research Article
                Medicine and Health Sciences
                Medical Conditions
                Infectious Diseases
                Viral Diseases
                Covid 19
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Coronaviruses
                SARS coronavirus
                SARS CoV 2
                Biology and life sciences
                Microbiology
                Medical microbiology
                Microbial pathogens
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                Coronaviruses
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                Medicine and health sciences
                Pathology and laboratory medicine
                Pathogens
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                Viral pathogens
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                Biology and life sciences
                Organisms
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                Coronaviruses
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                Biology and Life Sciences
                Anatomy
                Body Fluids
                Blood
                Medicine and Health Sciences
                Anatomy
                Body Fluids
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                Physiology
                Body Fluids
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                Custom metadata
                Data with a very low risk of re-identification and no particular sensitivity (“open access data”), such as aggregated patient data from the different cohorts is available via the BQC19 website ( www.BQC19.ca) or can be requested by email at: info@ 123456bqc19.ca . Upon completion of the study, the publicly available data will be deposited on a repository with the link provided in the comment section of the article. The stored biological materials will be accessed through a controlled system. Data that has a direct or high risk of re-identification will also go through a tightly controlled access process available at BQC19.ca and described in greater details in the manuscript.
                COVID-19

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