Multiancestry Genome-Wide Association Study of Early Childhood Caries

Abstract

Early childhood caries (ECC) is the most common noncommunicable childhood disease-an important health problem with known environmental and social/behavioral influences lacking consensus genetic risk loci. To address this knowledge gap, we conducted a genome-wide association study of ECC in a multiancestry population of U.S. preschool-age children (N = 6,103) ages 3 to 5 y participating in a community-based epidemiologic study of early childhood oral health. Calibrated examiners used International Caries Detection and Assessment System criteria to measure ECC; the primary trait was the number of primary tooth surfaces with caries experience (i.e., dmfs index). We estimated heritability and concordance rates and conducted genome-wide association analyses to estimate overall genetic effects as well as stratified by sex, household water fluoride, and dietary sugar and leveraged combined gene/gene-environment effects using 2-degree-of-freedom joint tests. Common genetic variants explained 24% of ECC phenotypic variance among unrelated individuals, while concordance rates were 0.64 (95% confidence interval [CI] = 0.42-0.79) among monozygotic twins and 0.44 (95% CI = 0.34-0.53) among first-degree relatives. Across all analyses, we identified 21 novel nonoverlapping genome-wide significant loci (P < 5 × 10^-8) and 1 genome-wide significant gene (TAAR6) associated with ECC. The taste receptor activity gene set, with known roles in chemosensing, bacterial recognition, and innate immunity in the oral cavity, was strongly associated with ECC. While no locus remained significant after studywise multiple-testing correction, 3 loci were nominally significant (P < 0.05) and directionally consistent in external cohorts of 285,248 adults (rs1442369, DLGAP1 and rs74606067, RP11-856F16.2) and 18,994 children (rs71327750, SLC41A3). Meanwhile, the strongest marker known to be associated with adult caries (rs1122171, tagging the long noncoding RNA PITX1-AS1) was nominally significant (P = 0.01) and directionally consistent with ECC in our study. Taken together, the results of this study add to the genomics knowledge base for early childhood caries, offer several plausible candidates for future mechanistic studies, and underscore the importance of accounting for sex and pertinent environmental exposures in genetic investigations.

Keywords: dental caries; gene-environment interaction; genetic variants; genetics; genomics; heritability; single nucleotide polymorphism.

Figure 1.

Summary of the study’s design and results. In approach 1, we conducted a GWAS in the entire sample. In approach 2, we conducted a joint 2-degree-of-freedom test to test single markers’ main and interaction effects jointly accounting for interactions with 3 environmental exposures: biological sex (male or female), fluoride exposure (optimal or suboptimal fluoride content of household water), and sugar exposure (frequency of daily consumption of sugary snacks and beverages in between meals). In approach 3, we conducted stratified GWAS for the 3 dichotomous environmental exposures. *Covariates in all association tests included age, sex, race/ethnicity, first 8 ancestry principal components, fluoride exposure, and sugar exposure. ^¥Further, 5 loci were independently genome-wide significant for the secondary ECC traits (Appendix Table 7). 2df, 2-degree-of-freedom; [E], environmental factor; GWAS, genome-wide association study; SNP, single nucleotide polymorphism.

Figure 2.

Regional association plots and summary of association results of the 3 genetic risk loci for ECC from the main discovery analysis (approach 1) in a multiancestry population of preschool-age children. (a) DLGAP1, (b) SLC1A5, and (c) KCNU1. Vertical axes illustrate association P values on the –log₁₀ scale, and horizontal axes represent chromosome positions. Purple diamonds denote the SNP with the strongest association signal (lead SNP) in the locus. Upward triangles denote positive betas or positive associations, downward triangles denote negative betas or inverse associations, and circles mark variants with P values > 0.05. Other SNPs in locus are colored based on their LD (all populations, 1000G data) with the lead SNP. Δd3-6mfs, change in the dmfs index per effect allele to which the estimated beta corresponds; b, beta coefficient; chr, chromosome; EA, effect allele; EAF, effect allele frequency; ECC, early childhood caries; EffN, effective sample size; n, sample size; OA, other allele; P, P value; pos, position; SE, standard error; SNP, single nucleotide polymorphism.

Figure 3.

Forest plots demonstrating heterogeneity of genetic effect due to (A) sex, (B) fluoride exposure, and (C) sugar exposure for the top loci identified in the 3 stratified GWASs (approach 3). The triangles and circles represent the estimates of association with ECC, and the error bars represent the corresponding 95% confidence intervals. Loci are labeled as the nearest gene and ordered according to their magnitude of association among females, optimal fluoride-level stratum, and the high-sugar stratum, respectively. ECC, early childhood caries; GWAS, genome-wide association study.