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.Luan, J.Gustafsson, S.Randall, J.C.Vedantam, S.Workalemahu, T.Kilpelainen, T.O.Scherag, A.Esko, T.Kutalik, Z.Heid, I.M.et al.2016-11-222016-11-222014Nature Protocols, 2014; 9(5):1192-12121754-21891750-2799http://hdl.handle.net/2440/102703Rigorous 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.en© 2014 Nature America Inc. All rights reserved.Genetic Investigation of Anthropometric Traits (GIANT) Consortium; quality control; software; meta-analysis as topic; genome-wide association studyJournal article003002691910.1038/nprot.2014.071000335014500015159721