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Meta‐analysis of gene‐environment interaction: joint estimation of SNP and SNP × environment regression coefficients
Author(s) -
Manning Alisa K.,
LaValley Michael,
Liu ChingTi,
Rice Kenneth,
An Ping,
Liu Yongmei,
Miljkovic Iva,
RasmussenTorvik Laura,
Harris Tamara B.,
Province Michael A.,
Borecki Ingrid B.,
Florez Jose C.,
Meigs James B.,
Cupples L. Adrienne,
Dupuis Josée
Publication year - 2011
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.20546
Subject(s) - snp , genome wide association study , meta analysis , single nucleotide polymorphism , genetics , trait , statistics , genetic association , gene–environment interaction , biology , tag snp , quantitative trait locus , multivariate statistics , computational biology , computer science , mathematics , gene , genotype , medicine , programming language
Abstract Introduction : Genetic discoveries are validated through the meta‐analysis of genome‐wide association scans in large international consortia. Because environmental variables may interact with genetic factors, investigation of differing genetic effects for distinct levels of an environmental exposure in these large consortia may yield additional susceptibility loci undetected by main effects analysis. We describe a method of joint meta‐analysis (JMA) of SNP and SNP by Environment (SNP × E) regression coefficients for use in gene‐environment interaction studies. Methods : In testing SNP × E interactions, one approach uses a two degree of freedom test to identify genetic variants that influence the trait of interest. This approach detects both main and interaction effects between the trait and the SNP. We propose a method to jointly meta‐analyze the SNP and SNP × E coefficients using multivariate generalized least squares. This approach provides confidence intervals of the two estimates, a joint significance test for SNP and SNP × E terms, and a test of homogeneity across samples. Results : We present a simulation study comparing this method to four other methods of meta‐analysis and demonstrate that the JMA performs better than the others when both main and interaction effects are present. Additionally, we implemented our methods in a meta‐analysis of the association between SNPs from the type 2 diabetes‐associated gene PPARG and log‐transformed fasting insulin levels and interaction by body mass index in a combined sample of 19,466 individuals from five cohorts. Genet. Epidemiol. 35:11–18, 2011. © 2010 Wiley‐Liss, Inc.