» Articles » PMID: 23657481

Meta-analysis Methods for Genome-wide Association Studies and Beyond

Overview
Journal Nat Rev Genet
Specialty Genetics
Date 2013 May 10
PMID 23657481
Citations 294
Authors
Affiliations
Soon will be listed here.
Abstract

Meta-analysis of genome-wide association studies (GWASs) has become a popular method for discovering genetic risk variants. Here, we overview both widely applied and newer statistical methods for GWAS meta-analysis, including issues of interpretation and assessment of sources of heterogeneity. We also discuss extensions of these meta-analysis methods to complex data. Where possible, we provide guidelines for researchers who are planning to use these methods. Furthermore, we address special issues that may arise for meta-analysis of sequencing data and rare variants. Finally, we discuss challenges and solutions surrounding the goals of making meta-analysis data publicly available and building powerful consortia.

Citing Articles

Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers.

Bravo J, Zhang L, Benayoun B Transl Med Aging. 2025; 9:25-40.

PMID: 40051556 PMC: 11883834. DOI: 10.1016/j.tma.2025.02.001.


Cross-ancestry genome-wide association study and systems-level integrative analyses implicate new risk genes and therapeutic targets for depression.

Li Y, Dang X, Chen R, Teng Z, Wang J, Li S Nat Hum Behav. 2025; .

PMID: 39994458 DOI: 10.1038/s41562-024-02073-6.


Multi-ancestry genome-wide association analyses: a comparison of meta- and mega-analyses in the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study.

Kuang A, Hivert M, Hayes M, Lowe Jr W, Scholtens D BMC Genomics. 2025; 26(1):65.

PMID: 39849370 PMC: 11755808. DOI: 10.1186/s12864-025-11229-1.


A meta-analysis of genome-wide association studies to identify candidate genes associated with feed efficiency traits in pigs.

Silva M, Veroneze R, Marques D, Silva D, Machado I, Brito L J Anim Sci. 2025; 103.

PMID: 39847436 PMC: 11833465. DOI: 10.1093/jas/skaf010.


metaGE: Investigating genotype x environment interactions through GWAS meta-analysis.

De Walsche A, Vergne A, Rincent R, Roux F, Nicolas S, Welcker C PLoS Genet. 2025; 21(1):e1011553.

PMID: 39792927 PMC: 11756807. DOI: 10.1371/journal.pgen.1011553.


References
1.
Pereira T, Patsopoulos N, Salanti G, Ioannidis J . Discovery properties of genome-wide association signals from cumulatively combined data sets. Am J Epidemiol. 2009; 170(10):1197-206. PMC: 2800267. DOI: 10.1093/aje/kwp262. View

2.
Morris A, Zeggini E . An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol. 2009; 34(2):188-93. PMC: 2962811. DOI: 10.1002/gepi.20450. View

3.
. Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet. 2010; 42(5):441-7. PMC: 2914600. DOI: 10.1038/ng.571. View

4.
Ioannidis J, Thomas G, Daly M . Validating, augmenting and refining genome-wide association signals. Nat Rev Genet. 2009; 10(5):318-29. PMC: 7877552. DOI: 10.1038/nrg2544. View

5.
Behrens G, Winkler T, Gorski M, Leitzmann M, Heid I . To stratify or not to stratify: power considerations for population-based genome-wide association studies of quantitative traits. Genet Epidemiol. 2011; 35(8):867-79. DOI: 10.1002/gepi.20637. View