Quality control and conduct of genome-wide association meta-analyses

Thomas W Winkler; Felix R Day; Damien C Croteau-Chonka; Andrew R Wood; Adam E Locke; Reedik Mägi; Teresa Ferreira; Tove Fall; Mariaelisa Graff; Anne E Justice; Jian'an Luan; Stefan Gustafsson; Joshua C Randall; Sailaja Vedantam; Tsegaselassie Workalemahu; Tuomas Kilpeläinen; André Scherag; Tonu Esko; Zoltán Kutalik; Iris M Heid; Ruth J F Loos

doi:10.1038/nprot.2014.071

Quality control and conduct of genome-wide association meta-analyses

Authors:

Winkler, Thomas W ;
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Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg
Day, Felix R ;
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Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
Croteau-Chonka, Damien C ;
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Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA.
Wood, Andrew R ;
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Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Locke, Adam E ;
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Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Mägi, Reedik ;
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University of Tartu
Ferreira, Teresa ;
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University of Oxford
Fall, Tove ;
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Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University
Graff, Mariaelisa ;
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Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA.
Justice, Anne E ;
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Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA.
Luan, Jian'an ;
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Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
Gustafsson, Stefan ;
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Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University
Randall, Joshua C ;
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Wellcome Trust Sanger Institute
Vedantam, Sailaja ;
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Boston Children's Hospital, Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research
Workalemahu, Tsegaselassie ;
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Harvard School of Public Health
Kilpeläinen, Tuomas ;
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0000-0002-8349-3028
Section for Metabolic Genetics, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Københavns Universitet
Scherag, André ;
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University of Duisburg-Essen
Esko, Tonu ;
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Boston Children's Hospital, Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research
Kutalik, Zoltán ;
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Department of Medical Genetics, University of Lausanne
Heid, Iris M ;
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Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg
Loos, Ruth J F
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The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai

DOI:

10.1038/nprot.2014.071

Abstract:

Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.

Type:

Journal article

Language:

English

Published in:

Nature Protocols (online), 2014, Vol 9, Issue 5, p. 1192-1212

Keywords:

Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Genome-Wide Association Study; Meta-Analysis as Topic; Quality Control; Software

Main Research Area:

Medical science

Publication Status:

Published

Review type:

Peer Review

Submission year:

2014

Scientific Level:

Scientific

ID:

266902305

Quality control and conduct of genome-wide association meta-analyses

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