학술논문
Quality control and conduct of genome-wide association meta-analyses
Document Type
Report
Author
Winkler, Thomas W.; Day, Felix R.; Croteau-Chonka, Damien C.; Wood, Andrew R.; Locke, Adam E.; Magi, Reedik; Ferreira, Teresa; Fall, Tove; Graff, Mariaelisa; Justice, Anne E.; Luan, Jian'an; Gustafsson, Stefan; Randall, Joshua C.; Vedantam, Sailaja; Workalemahu, Tsegaselassie; Kilpelainen, Tuomas O.; Scherag, Andre; Esko, Tonu; Kutalik, Zoltan; Heid, Iris M.; Loos, Ruth J.F.
Source
Nature Protocols. May 1, 2014, Vol. 9 Issue 5, p1192, 21 p.
Subject
Language
English
ISSN
1754-2189
Abstract
INTRODUCTION Background The genome-wide association study (GWAS) approach has been extremely successful in pinpointing the association of common genetic variants with diseases or disease-related quantitative phenotypes (1,2). However, given the [...]
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.
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.