Quality Control and Conduct of Genome-wide Association Meta-analyses

Overview

Journal Nat Protoc

Specialties Biology
Pathology
Science

Date 2014 Apr 26

PMID 24762786

Citations 277

Authors

Thomas W Winkler

Felix R Day

Damien C Croteau-Chonka

Andrew R Wood

Adam E Locke

Reedik Magi

Teresa Ferreira

Tove Fall

Mariaelisa Graff

Anne E Justice

Jianan Luan

Stefan Gustafsson

Joshua C Randall

Sailaja Vedantam

Tsegaselassie Workalemahu

Tuomas O Kilpelainen

Andre Scherag

Tonu Esko

Zoltan Kutalik

Iris M Heid

Ruth J F Loos

Affiliations

Soon will be listed here.

Abstract

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.

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