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Fig. 2 | BMC Genetics

Fig. 2

From: Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression

Fig. 2

Type I error of weighted/unweighted GRS and single SNPs analysis with increasing sample size. Power comparison for the combined analysis of interaction effects between 6 SNPs and a single continuous environmental exposure (Design 1 (D1)) and in two extended scenarios: 1) “D1 + 42 correlated SNPs” contains the 6 SNPs from Design 1 and 42 SNPs that are in a high Linkage Disequilibrium with these SNPs and 2) “D1 + 20 noise SNPs” contains the 6 SNPs from Design 1 and 20 SNPs that are not associated with the phenotype. Comparison of weighted GRS (weights from elastic net regression with penalty weight α = 0.5 (EN05)), unweighted GRS and single SNPs analysis with Bonferroni correction (best SNP; SNP with the smallest p-value) in scenarios with increasing effect size of the interaction term (a) Mean (OR(GxE) = 1.01, b) Mean OR(GxE) = 1.04, c) Mean OR(GxE) = 1.05) and increasing sample size of 400, 700 and 1000 (1000 replications)

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