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

TitleQuality control and conduct of genome-wide association meta-analyses.
Publication TypeJournal Article
Year of Publication2014
AuthorsWinkler TW, Day FR, Croteau-Chonka DC, Wood AR, Locke AE, Mägi R, Ferreira T, Fall T, Graff M, Justice AE, Luan J'an, Gustafsson S, Randall JC, Vedantam S, Workalemahu T, Kilpeläinen TO, Scherag A, Esko T, Kutalik Z, Heid IM
Secondary AuthorsLoos RJF
Corporate AuthorsGenetic Investigation of Anthropometric Traits(GIANT) Consortium
JournalNat Protoc
Volume9
Issue5
Pagination1192-212
Date Published2014 May
ISSN1750-2799
KeywordsGenome-Wide Association Study, Meta-Analysis as Topic, Quality Control, Software
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.

DOI10.1038/nprot.2014.071
Alternate JournalNat Protoc
PubMed ID24762786
PubMed Central IDPMC4083217
Grant ListDK078150 / DK / NIDDK NIH HHS / United States
CZB/4/672 / / Chief Scientist Office / United Kingdom
R01DK075787 / DK / NIDDK NIH HHS / United States
U106179472 / / Medical Research Council / United Kingdom
G1000143 / / Medical Research Council / United Kingdom
MR/J012165/1 / / Medical Research Council / United Kingdom
R01 DK075787 / DK / NIDDK NIH HHS / United States
MC_UU_12015/1 / / Medical Research Council / United Kingdom
R37 HL066289 / HL / NHLBI NIH HHS / United States
MC_U106179471 / / Medical Research Council / United Kingdom
097117 / / Wellcome Trust / United Kingdom
MC_UU_12015/2 / / Medical Research Council / United Kingdom
14136 / / Cancer Research UK / United Kingdom
U106179471 / / Medical Research Council / United Kingdom
MC_U106179472 / / Medical Research Council / United Kingdom
G0401527 / / Medical Research Council / United Kingdom
MR/K013351/1 / / Medical Research Council / United Kingdom
T32 HL007055 / HL / NHLBI NIH HHS / United States
R01 DK078150 / DK / NIDDK NIH HHS / United States
T32 HL007427 / HL / NHLBI NIH HHS / United States