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      Collider bias undermines our understanding of COVID-19 disease risk and severity

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          Abstract

          Numerous observational studies have attempted to identify risk factors for infection with SARS-CoV-2 and COVID-19 disease outcomes. Studies have used datasets sampled from patients admitted to hospital, people tested for active infection, or people who volunteered to participate. Here, we highlight the challenge of interpreting observational evidence from such non-representative samples. Collider bias can induce associations between two or more variables which affect the likelihood of an individual being sampled, distorting associations between these variables in the sample. Analysing UK Biobank data, compared to the wider cohort the participants tested for COVID-19 were highly selected for a range of genetic, behavioural, cardiovascular, demographic, and anthropometric traits. We discuss the mechanisms inducing these problems, and approaches that could help mitigate them. While collider bias should be explored in existing studies, the optimal way to mitigate the problem is to use appropriate sampling strategies at the study design stage.

          Abstract

          Many published studies of the current SARS-CoV-2 pandemic have analysed data from non-representative samples from populations. Here, using UK BioBank samples, Gibran Hemani and colleagues discuss the potential for such studies to suffer from collider bias, and provide suggestions for optimising study design to account for this.

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          lavaan: AnRPackage for Structural Equation Modeling

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            The UK Biobank resource with deep phenotyping and genomic data

            The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at recruitment. The open resource is unique in its size and scope. A rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. Follow-up information is provided by linking health and medical records. Genome-wide genotype data have been collected on all participants, providing many opportunities for the discovery of new genetic associations and the genetic bases of complex traits. Here we describe the centralized analysis of the genetic data, including genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation that increases the number of testable variants to around 96 million. Classical allelic variation at 11 human leukocyte antigen genes was imputed, resulting in the recovery of signals with known associations between human leukocyte antigen alleles and many diseases.
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              Robust causal inference using directed acyclic graphs: the R package ‘dagitty’

              Directed acyclic graphs (DAGs), which offer systematic representations of causal relationships, have become an established framework for the analysis of causal inference in epidemiology, often being used to determine covariate adjustment sets for minimizing confounding bias. DAGitty is a popular web application for drawing and analysing DAGs. Here we introduce the R package 'dagitty', which provides access to all of the capabilities of the DAGitty web application within the R platform for statistical computing, and also offers several new functions. We describe how the R package 'dagitty' can be used to: evaluate whether a DAG is consistent with the dataset it is intended to represent; enumerate 'statistically equivalent' but causally different DAGs; and identify exposure-outcome adjustment sets that are valid for causally different but statistically equivalent DAGs. This functionality enables epidemiologists to detect causal misspecifications in DAGs and make robust inferences that remain valid for a range of different DAGs. The R package 'dagitty' is available through the comprehensive R archive network (CRAN) at [https://cran.r-project.org/web/packages/dagitty/]. The source code is available on github at [https://github.com/jtextor/dagitty]. The web application 'DAGitty' is free software, licensed under the GNU general public licence (GPL) version 2 and is available at [http://dagitty.net/].
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                Author and article information

                Contributors
                g.hemani@bristol.ac.uk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                12 November 2020
                12 November 2020
                2020
                : 11
                : 5749
                Affiliations
                [1 ]GRID grid.5337.2, ISNI 0000 0004 1936 7603, Medical Research Council Integrative Epidemiology Unit, , University of Bristol, ; Bristol, BS8 2BN UK
                [2 ]GRID grid.5337.2, ISNI 0000 0004 1936 7603, Population Health Sciences, Bristol Medical School, , University of Bristol, Oakfield House, Oakfield Grove, ; Bristol, BS8 2BN UK
                [3 ]GRID grid.5947.f, ISNI 0000 0001 1516 2393, K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, , NTNU, Norwegian University of Science and Technology, ; Trondheim, Norway
                Author information
                http://orcid.org/0000-0003-0481-3175
                http://orcid.org/0000-0001-8178-6815
                http://orcid.org/0000-0002-7897-6180
                http://orcid.org/0000-0003-2906-4035
                http://orcid.org/0000-0003-4655-4511
                http://orcid.org/0000-0002-1407-8314
                http://orcid.org/0000-0002-1010-8926
                http://orcid.org/0000-0002-2460-0508
                http://orcid.org/0000-0003-0920-1055
                Article
                19478
                10.1038/s41467-020-19478-2
                7665028
                33184277
                3eab4f6e-15fc-4094-af83-73feae26bff5
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 28 May 2020
                : 8 October 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/100004440, Wellcome Trust (Wellcome);
                Award ID: 208806/Z/17/Z
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                statistical methods,infectious diseases,epidemiology,risk factors
                Uncategorized
                statistical methods, infectious diseases, epidemiology, risk factors

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