Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate

Abstract

Nonsyndromic cleft palate (CP) is a common birth defect with a complex and heterogeneous etiology involving both genetic and environmental risk factors. We conducted a genome-wide association study (GWAS) using 550 case-parent trios, ascertained through a CP case collected in an international consortium. Family-based association tests of single nucleotide polymorphisms (SNP) and three common maternal exposures (maternal smoking, alcohol consumption, and multivitamin supplementation) were used in a combined 2 df test for gene (G) and gene-environment (G × E) interaction simultaneously, plus a separate 1 df test for G × E interaction alone. Conditional logistic regression models were used to estimate effects on risk to exposed and unexposed children. While no SNP achieved genome-wide significance when considered alone, markers in several genes attained or approached genome-wide significance when G × E interaction was included. Among these, MLLT3 and SMC2 on chromosome 9 showed multiple SNPs resulting in an increased risk if the mother consumed alcohol during the peri-conceptual period (3 months prior to conception through the first trimester). TBK1 on chr. 12 and ZNF236 on chr. 18 showed multiple SNPs associated with higher risk of CP in the presence of maternal smoking. Additional evidence of reduced risk due to G × E interaction in the presence of multivitamin supplementation was observed for SNPs in BAALC on chr. 8. These results emphasize the need to consider G × E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as nonsyndromic CP.

Figure 1

Double Manhattan plots for SNP effects ignoring maternal exposures (lower half) and considering G and G×E interaction for three maternal exposures. Blue dots represent –log₁₀(p-value) from 1 df test of G×E interaction alone; red dots represent – log₁₀(p-value) from 2 df test of G and G×E interaction. Only autosomal SNPs showing p<0.0001 for one of these two tests are displayed. Dashed lines connect SNP showing this level of significance in one test considering G×E interaction with their corresponding p-value when interaction is ignored. Panel A: Results for GxMaternal Alcohol Consumption interaction; Panel B: Results for GxMaternal Smoking interaction; Panel C: Results for GxMaternal Vitamin Use interaction.

Figure 2

Estimated OR(CP|G no E) and OR(CP|G and E) for maternal alcohol consumption from logistic regression on 550 case-parent trios. P-values from 1 df LRT for G×E interaction are shown along the X axis. Panel A: Estimated OR(CP|G no E) and OR(CP|G and E) for 7 SNPs in MLLT3. Panel B: Estimated OR(CP|G no E) and OR(CP|G and E) for 7 SNPs in SMC2.

Figure 3

Estimated OR(CP|G no E) and OR(CP|G and E) considering G×E interaction with maternal smoking in logistic regression on 550 case-parent trios. Panel A: Estimated OR(CP|G no E) and OR(CP|G and E) for 9 SNPs in TBK1. P-values from 2 df LRT for G and G×E interaction plus that from 1 df LRT for G×E interaction are shown along the X axis. Panel B: Estimated OR(CP|G no E) and OR(CP|G and E) for 10 SNPs in ZNF236. P-values from 1 df LRT for G×E interaction are shown along the X axis.

Figure 4

Estimated OR(CP|G no E) and OR(CP|G and E) for 11 SNPs in BAALC considering G×E interaction with maternal vitamin supplementation in logistic regression on 550 CP case-parent trios. P-values from 1 df LRT for G×E interaction are shown along the X axis.