Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions
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- Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions
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Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G×E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G×E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ = 0.401 for triglycerides, and ρ = 0.236 for BMI) compared to all SNPs. When Pv and Pm were compared for all pruned SNPs, only BMI was statistically significant (Spearman's ρ = 0.010). Overall, SNPs with established marginal effects were overrepresented in the nominally significant part of the Pv distribution (Pbinomial <0.05). SNPs from the top 1% of the Pm distribution for BMI had more significant Pv values (PMann-Whitney = 1.46×10-5), and the odds ratio of SNPs with nominally significant (<0.05) Pm and Pv was 1.33 (95% CI: 1.12, 1.57) for BMI. Moreover, BMI SNPs with nominally significant G×E interaction P-values (Pint<0.05) were enriched with nominally significant Pv values (Pbinomial = 8.63×10-9 and 8.52×10-7 for SNP × smoking and SNP × physical activity, respectively). We conclude that some loci with strong marginal effects may be good candidates for G×E, and variance-based prioritization can be used to identify them.
Original language | English |
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Article number | e1006812 |
Journal | P L o S Genetics |
Volume | 13 |
Issue number | 6 |
Number of pages | 15 |
ISSN | 1553-7390 |
DOIs | |
Publication status | Published - Jun 2017 |
- Body Mass Index, Cholesterol, HDL, Cholesterol, LDL, European Continental Ancestry Group, Female, Gene-Environment Interaction, Genetic Heterogeneity, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Male, Obesity, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk Factors, Smoking, Journal Article, Meta-Analysis
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