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Nat Protoc DOI:10.1038/nprot.2014.071

Quality 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, Loos, RJF
Corporate AuthorsGenetic Investigation of Anthropometric Traits (GIANT) Consortium
JournalNat Protoc
Volume9
Issue5
Pages1192-212
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.

URLhttp://dx.doi.org/10.1038/nprot.2014.071
DOI10.1038/nprot.2014.071
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/24762786?dopt=Abstract

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