Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate

Abstract

Although multiple genes have been identified as genetic risk factors for isolated, non-syndromic cleft lip with/without cleft palate (CL/P), a complex and heterogeneous birth defect, interferon regulatory factor 6 gene (IRF6) is one of the best documented genetic risk factors. In this study, we tested for association between markers in IRF6 and CL/P in 326 Chinese case-parent trios, considering gene-environment interaction for two common maternal exposures, and parent-of-origin effects. CL/P case-parent trios from three sites in mainland China and Taiwan were genotyped for 22 single nucleotide polymorphisms (SNPs) in IRF6. The transmission disequilibrium test was used to test for marginal effects of individual SNPs. We used PBAT to screen the SNPs and haplotypes for gene-environment (G×E) interaction and conditional logistic regression models to quantify effect sizes for SNP-environment interaction. After Bonferroni correction, 14 SNPs showed statistically significant association with CL/P. Evidence of G×E interaction was found for both maternal exposures, multivitamin supplementation and environmental tobacco smoke (ETS). Two SNPs showed evidence of interaction with multivitamin supplementation in conditional logistic regression models (rs2076153 nominal P=0.019, rs17015218 nominal P=0.012). In addition, rs1044516 yielded evidence for interaction with maternal ETS (nominal P=0.041). Haplotype analysis using PBAT also suggested interaction between SNPs in IRF6 and both multivitamin supplementation and ETS. However, no evidence for maternal genotypic effects or significant parent-of-origin effects was seen in these data. These results suggest IRF6 gene may influence risk of CL/P through interaction with multivitamin supplementation and ETS in the Chinese population.

Fig. 1

Significance of individual single nucleotide polymorphisms (SNPs) and sliding window haplotypes for the interferon regulatory factor 6 (IRF6) gene in 326 nonsyndromic cleft lip with or without cleft palate trios. The −log10 (empirical P value) for the overall test for an individual SNP (dots) and for sliding windows of haplotypes of two to five SNPs (dots connected by lines) is presented. Only haplotypes with P values < 0.001 are shown here. The plot was produced using snp.plotter (Luna and Nicodemus 2007)

Fig. 2

Testing for gene–environment interaction (G × E) for common maternal exposures in 326 CL/P case–parent trios from Chinese populations. Triangles represent the gene–environmental interaction 2 df test of G and G × E interaction, squares represent the 1 df test of G × E only. Haplotypes of 2- and 3-loci are connected by dashed lines (only nominally significant haplotypes P < 10⁻³). SNPs in bold showed significant P values (nominal P < 0.05) for genetic effects ignoring environmental exposures

Fig. 3

Odds ratios (OR) and 95% confidence intervals (CI) for estimated effects of gene–multivitamin supplementation interaction at four SNPs in IRF6. Odds ratios and CIs are drawn on a logarithmic scale. The ORs and 95% CI were obtained from conditional logistic regression using additive model. Filled circles represent the ORs of being a case with one copy of the risk allele and without exposure to maternal vitamin supplementation (for rs2076153 and rs7552506 the reference allele is the minor allele and for rs599021 and rs861019, the reference allele is the major allele). Open circles represent the odds ratios of being a case with one copy of the risk allele and being exposed to maternal vitamin supplementation. P values from the likelihood ratio test (LRT) with 1 degree of freedom testing the significance of gene–multivitamin supplementation interaction are showed for each SNP