Quality control and conduct of genome-wide association meta-analyses
Date
2014
Authors
Winkler, T.W.
Day, F.R.
Croteau-Chonka, D.C.
Wood, A.R.
Locke, A.E.
Maegi, R.
Ferreira, T.
Fall, T.
Graff, M.
Justice, A.E.
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Journal article
Citation
Nature Protocols, 2014; 9(5):1192-1212
Statement of Responsibility
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
Conference Name
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.
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© 2014 Nature America Inc. All rights reserved.