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Type: Journal article
Title: Quality control and conduct of genome-wide association meta-analyses
Author: Winkler, T.
Day, F.
Croteau-Chonka, D.
Wood, A.
Locke, A.
Maegi, R.
Ferreira, T.
Fall, T.
Graff, M.
Justice, A.
Luan, J.
Gustafsson, S.
Randall, J.
Vedantam, S.
Workalemahu, T.
Kilpelainen, T.
Scherag, A.
Esko, T.
Kutalik, Z.
Heid, I.
et al.
Citation: Nature Protocols, 2014; 9(5):1192-1212
Publisher: Nature Publishing Group
Issue Date: 2014
ISSN: 1754-2189
Statement of
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 O Kilpeläinen, André Scherag, Tonu Esko, Zoltán Kutalik, Iris M Heid, Ruth J F Loos, the Genetic Investigation of Anthropometric Traits, GIANT, Consortium
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.
Keywords: Genetic Investigation of Anthropometric Traits (GIANT) Consortium; quality control; software; meta-analysis as topic; genome-wide association study
Rights: © 2014 Nature America Inc. All rights reserved.
RMID: 0030026919
DOI: 10.1038/nprot.2014.071
Appears in Collections:Translational Health Science publications

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