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Nature protocols DOI:10.1038/nprot.2014.071

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

Publication TypeJournal Article
Year of Publication2014
AuthorsWinkler, TW, Day, FR, Croteau-Chonka, DC, Wood, AR, Locke, AE, Mägi, R, Ferreira, T, Fall, T, Graff, M, Justice, AE, Luan, J, Gustafsson, S, Randall, JC, Vedantam, S, Workalemahu, T, Kilpeläinen, TO, Scherag, A, Esko, T, Kutalik, Z, Heid, IM, Loos, RJ, Genetic Investigation of ANthropometric Traits (GIANT), C
JournalNature protocols
Date Published2014/05/01

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.