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

Research output: Contribution to journalJournal articleResearchpeer-review

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 Kilpeläinen, André Scherag, Tonu Esko, Zoltán Kutalik, Iris M Heid & 2 others Ruth J F Loos, Genetic Investigation of Anthropometric Traits (GIANT) Consortium

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.
Original languageEnglish
JournalNature Protocols (Online)
Issue number5
Pages (from-to)1192-1212
Number of pages21
Publication statusPublished - May 2014

ID: 108759875