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

TY - JOUR

T1 - Quality control and conduct of genome-wide association meta-analyses

AU - Winkler, Thomas W.

AU - Day, Felix R.

AU - Croteau-Chonka, Damien C.

AU - Wood, Andrew R.

AU - Locke, Adam E.

AU - Mägi, Reedik

AU - Ferreira, Teresa

AU - Fall, Tove

AU - Graff, Mariaelisa

AU - Justice, Anne E.

AU - Luan, Jian'an

AU - Gustafsson, Stefan

AU - Randall, Joshua C.

AU - Vedantam, Sailaja

AU - Workalemahu, Tsegaselassie

AU - Kilpeläinen, Tuomas O.

AU - Scherag, André

AU - Esko, Tonu

AU - Kutalik, Zoltán

AU - Heid, Iris M.

AU - Loos, Ruth J. F.

AU - Genetic Investigation of ANthropometric Traits (GIANT) Consortium

AU - Connell, John M.

AU - Morris, Andrew D.

AU - Palmer, Colin N. A.

PY - 2014/5

Y1 - 2014/5

N2 - 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.

AB - 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.

KW - Genome-Wide Association Study

KW - Meta-Analysis as Topic

KW - Quality Control

KW - Software

U2 - 10.1038/nprot.2014.071

DO - 10.1038/nprot.2014.071

M3 - Article

C2 - 24762786

SN - 1754-2189

VL - 9

SP - 1192

EP - 1212

JO - Nature Protocols

JF - Nature Protocols

IS - 5

ER -