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

• DOI: 10.1038/nprot.2014.071
• Publication Date: 2014-04-24T15:34:52Z
• Authors: Thomas W Winkler; Felix R Day; Damien C Croteau-...; 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 Wor...; Tuomas O Kilpeläinen; André Scherag; Tonu Esko; Zoltán Kutalik; Iris M Heid; Ruth J F Loos
• Keywords: Genome-wide Association Study

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 [1] organizational aspects of GWAMAs, and for [2] 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 use of a powerful and flexible software package called EasyQC. For consortia of comparable size to the GIANT consortium, the present protocol takes a minimum of about 10 months to complete.