Exploring the genomic basis of early childhood caries: a pilot study

Genetic variations in exon 10 of ENAM and their association with early childhood caries

OBJECTIVE

Enamelin is the largest enamel matrix protein encoded by the ENAM gene. The primary purpose of this study was to identify genetic variants in ENAM exon 10 that can alter susceptibility to early childhood caries (ECC).

METHODS

This case-control study included 248 children aged 3-6 years, with 124 children diagnosed with ECC in the case group and 124 children without caries in the control group. Questionnaires were used to record demographic data, socioeconomic status, hygienic practices, and feeding practices, and a 24-h diet diary was kept. Seven polymorphisms (rs7671281, rs1738668322, rs3796703, rs3796704, rs759376039, rs775159311, and rs1738678483) in ENAM exon 10 were sequenced.

RESULTS

The heterozygous CT genotype of rs7671281 was significantly more common in the case group compared to the control group (odds ratio [OR], 6.1765; 95% confidence interval [CI], 2.05-18.58; P = 0.0006). Under the dominant model, the TT genotype of rs7671281 was significantly more common in the control group (OR, 6.47; 95% CI, 2.15-19.39; P < 0.001). The AG genotype of rs3796704 was significantly more common in the case group than in the control group (OR, 5.705; 95% CI, 1.60-20.25; P = 0.006). Under the dominant model, the GG genotype of rs3796704 was significantly more common in children without caries than in children with caries (OR, 6.84; 95% CI, 1.96-23.90; P < 0.001).

CONCLUSIONS

The C allele of rs7671281 and the A allele of rs3796704 can increase susceptibility to ECC.

Probabilistic graphical modelling of early childhood caries development

In order to develop a statistical model for complex interactions among factors affecting early childhood caries development (ECC), 234 children from the "XXXX oral growth longitudinal study" were analysed at ages 3, 4 and 5. A questionnaire for children's parents (clinical history, nutritional and oral hygiene habits) and clinical oral examinations were recorded each year. The probabilistic dependence structure on the most significant factors was modelled with an Undirected Graphical Model (UGM or Markov random fields) which provides a probabilistic reasoning approach for the establishment of multi-way associations. The best fitting UGM was estimated through the maximum likelihood principle and two-way factor associations were verified through Fisher's exact statistical hypothesis tests for count data. The effect of sugar intake on caries incidence is mediated by oral hygiene; for caries incidence, oral hygiene quality is more relevant than toothbrushing time; the effect of pacifier on caries incidence is statistically significant only when considered in combination with breastfeeding time. Among behavioural ECC risk factors, the quality of oral hygiene, and not the toothbrushing frequency, is a primary factor that modulates the sugar intake in his primary role of the ECC developer. School-based oral health programs for ECC prevention should be improved with supervised toothbrushing program. UGM analysis could improve the school-based oral health programs with more effective and efficient prevention strategies based on the hierarchical interactions among the ECC risk factors. Oral hygiene plays a pivotal role in early childhood caries and can modulate positively or negatively their development. Supervised toothbrushing is a crucial intervention to be included in the daily educational and clinical practice and in the school-based oral health promotion programs. Trial registration: Clinical trial registration number: NCT02798809.

Subtypes of early childhood caries predict future caries experience

OBJECTIVES

To test whether postulated subtypes of early childhood caries (ECC) are predictive of subsequent caries experience in a population-based cohort of Swedish children.

METHODS

The study included children aged between 3 and 5 years at study entry with dental records available for at least 5 years of follow-up. Dental record data were retrieved from the Swedish Quality Registry for Caries and Periodontal disease (SKaPa) for the initial and follow-up visits. Participants who had ECC at study entry were assigned to one of five ECC subtypes (termed classes 1-5) using latent class modelling of tooth surface-level caries experience. Subsequent experience of caries was assessed using the decayed, missing and filled surfaces indices (dmfs/DMFS) at follow-up visits, and compared between ECC subtypes using logistic and negative binomial regression modelling.

RESULTS

The study included 128 355 children who had 3 or more dental visits spanning at least 5 years post-baseline. Of these children, 31 919 had caries at the initial visit. Baseline ECC subtype was associated with differences in subsequent disease experience. As an example, 83% of children who had a severe form of ECC at age 5 went on to have caries in the permanent dentition by the end of the study, compared to 51% of children who were caries-free at age 5 (adjusted odds ratio of 4.9 for new disease at their third follow-up).

CONCLUSIONS

ECC subtypes assigned at a baseline visit are associated with differences in subsequent caries experience in both primary and permanent teeth. This suggests that the development and future validation of an ECC classification can be used in addition to current prediction tools to help identify children at high risk of developing new caries lesions throughout childhood and adolescence.

Potential risk factors and genetic variants associated with dental caries incidence in Appalachia using genome-wide survival analysis

OBJECTIVE

The aim of this study was to identify the potential risk factors and genetic variants associated with dental caries incidence using survival analysis.

METHODS

The Center for Oral Health Research in Appalachia recruited and prospectively followed pregnant women and their children. A total of 909 children followed from birth for up to 7 years were included in this study. Annual intra-oral examinations were performed to assess dental caries experience including the approximate time to first caries incidence in the primary dentition. Cox proportional hazards models were used to assess the associations of time to first caries incidence with self-reported risk factors and 4.9 million genetic variants ascertained using a genome-wide genotyping array.

RESULTS

A total of 196 of 909 children (21.56%) had their first primary tooth caries event during follow-up. Household income, home water source, and mother's educational attainment were significantly associated with time to first caries incidence in the stepwise Cox model. The heritability (i.e., proportion of variance explained by genetics) of time to first caries was 0.54. Though no specific genetic variants were associated at the genome-wide significance level (P < 5E-8), we identified 14 loci at the suggestive significance level (5E-8 < P < 1E-5), some of which were located within or near genes with plausible biological functions in dental caries.

CONCLUSION

Our findings indicate that household income, home water source, and mother's educational attainment are independent risk factors for dental caries incidence. We nominate several suggestive loci for further investigation.

Association of Early Childhood Caries with Bitter Taste Receptors: A Meta-Analysis of Genome-Wide Association Studies and Transcriptome-Wide Association Study

Although genetics affects early childhood caries (ECC) risk, few studies have focused on finding its specific genetic determinants. Here, we performed genome-wide association studies (GWAS) in five cohorts of children (aged up to 5 years, total N = 2974, cohorts: Center for Oral Health Research in Appalachia cohorts one and two [COHRA1, COHRA2], Iowa Fluoride Study, Iowa Head Start, Avon Longitudinal Study of Parents and Children [ALSPAC]) aiming to identify genes with potential roles in ECC biology. We meta-analyzed the GWASs testing ~3.9 million genetic variants and found suggestive evidence for association at genetic regions previously associated with caries in primary and permanent dentition, including the β-defensin anti-microbial proteins. We then integrated the meta-analysis results with gene expression data in a transcriptome-wide association study (TWAS). This approach identified four genes whose genetically predicted expression was associated with ECC (p-values < 3.09 × 10−6; CDH17, TAS2R43, SMIM10L1, TAS2R14). Some of the strongest associations were with genes encoding members of the bitter taste receptor family (TAS2R); other members of this family have previously been associated with caries. Of note, we identified the receptor encoded by TAS2R14, which stimulates innate immunity and anti-microbial defense in response to molecules released by the cariogenic bacteria, Streptococcus mutans and Staphylococcus aureus. These findings provide insight into ECC genetic architecture, underscore the importance of host-microbial interaction in caries risk, and identify novel risk genes.

Multi-marker genetic association and interaction tests with interval-censored survival outcomes

The development of set-based genetic-survival association tests has been focusing on right-censored survival outcomes. However, interval-censored failure time data arise widely from health science studies, especially those on the development of chronic diseases. In this paper, we proposed a suite of set-based genetic association and interaction tests for interval-censored survival outcomes under a unified weighted-V-statistic framework. Besides dealing with interval censoring, the new tests can account for genetic effect heterogeneity and accommodate left truncation of survival outcomes. Simulation studies showed that the new tests perform well in terms of size and power under various scenarios and that the new interaction test is more powerful than the standard likelihood ratio test for testing gene-gene/gene-environment interactions. The practical utility of the developed tests was illustrated by a genome-wide association study of age to early childhood caries.

Replication of GWAS significant loci in a sub-Saharan African Cohort with early childhood caries: a pilot study

BACKGROUND

Early childhood caries (ECC) is a rapidly progressing form of dental infection and a significant public health problem, especially among socially and economically disadvantaged populations. This study aimed to assess the risk factors for ECC among a cohort of Sub-Saharan African children and to determine the role of genetics in the etiology of ECC.

METHODS

A sample of 691 children (338 with ECC, 353 without ECC, age < 6 years) was recruited from schools in Lagos, Nigeria. Socio-demographic, dental services utilization and infant dietary data were obtained with interviewer-administered questionnaire. Oral examination was conducted using the WHO oral health diagnostic criteria. Saliva samples were collected from the children for genetic analysis. Single nucleotide polymorphisms were selected from previous study for genotyping. Genetic association analyses to investigate the role of genetics in the etiology of ECC was done. Bivariate comparisons and Multivariate logistic regression analyses were conducted to assess associations between ECC and predictor variables, p < 0.05.

RESULTS

Of the 338 children with ECC, 64 (18.9%) had Severe-Early Childhood Caries (S-ECC). Children aged 48-59 months comprised the highest proportion of subjects with ECC (165; 48.8%) and S-ECC (24; 37.5%) while female subjects had higher dt (3.13 ± 2.56) and dmft values 3.27 ± 2.64. ECC was significantly more prevalent among children who were breastfed at night ≥ 12 months (OR 3.30; CI 0.39, 4.75), those with no previous dental visit (OR 1.71; CI 0.24, 2.77), those who used sweetened pacifiers (OR 1.85; CI 0.91, 3.79) and those who daily consumed sugar-sweetened drinks/snacks (OR 1.35; CI 0.09, 18.51). A suggestive increased risk for ECC (OR 1.26, p = 0. 0.0397) was observed for the genetic variant rs11239282 on chromosome 10. We also observed a suggestive reduced risk for ECC (OR 0.80, p = 0.03) for the rs131777 on chromosome 22. None of the genetic variants were significant after correction for multiple testing (Bonferroni p value p = 0.004).

CONCLUSIONS

Prolonged night-time breastfeeding, poor utilization of dental services and daily consumption of sugar were risk factors for ECC. Larger sample size is needed to confirm the results of the genetic analysis and to conduct genome wide studies in order to discover new risk loci for ECC.

Children's oral health-related behaviours and early childhood caries: A latent class analysis

OBJECTIVE

In this cross-sectional study in a large community-based sample of preschool-age children, we sought to identify distinct clusters of modifiable early childhood oral health-related behaviours (OHBs) and quantify their association with clinical and parent-reported measures of early childhood oral health.

METHODS

We relied upon a questionnaire (n = 8033; 11% in Spanish) and clinical oral health data (n = 6404; early childhood caries [ECC] prevalence = 54%] collected in the context of an epidemiologic study of early childhood oral health among 3- to 5-year-old children in North Carolina. Latent class analysis was used to identify clusters of modifiable OHBs based on parents' responses to 6 questionnaire items pertaining to their children's oral hygiene, diet and dental home. The optimal number of clusters was determined based on measures of model fit and interpretability. We examined associations of OHB clusters with clinical and parent-reported child oral health status (ie, ECC prevalence, severity and proportion with untreated disease) using bivariate association tests and multivariable regression modelling with marginal effects estimation accounting for clustered data. We used Mplus v.8.6 (Muthén & Muthén, Los Angeles, CA, USA) and Stata v.16.1 (StataCorp, College Station, TX, USA) for data analyses.

RESULTS

We identified 2 OHB clusters, a favourable (74%) and an unfavourable (26%) one. Children in the favourable OHB cluster had better oral hygiene practices (ie, tooth brushing frequency and fluoridated toothpaste use), lower consumption frequency of sugar-containing snacks and beverages, less frequent reports of night-time bottle-feeding history and a higher likelihood of a dental home. Children in the unfavourable cluster had significantly higher ECC prevalence (57% vs 53%), caries burden (mean dmfs = 9.3 vs 7.6), untreated disease (43% vs 33%) and worse parent-reported oral health status than the favourable cluster.

CONCLUSIONS

Our findings demonstrate the importance and utility of clustering common, modifiable ECC risk factors in population studies - health promotion efforts may centre on groups of people rather than individual behavioural risk factors.

Cohort Profile: ZOE 2.0-A Community-Based Genetic Epidemiologic Study of Early Childhood Oral Health

Early childhood caries (ECC) is an aggressive form of dental caries occurring in the first five years of life. Despite its prevalence and consequences, little progress has been made in its prevention and even less is known about individuals' susceptibility or genomic risk factors. The genome-wide association study (GWAS) of ECC ("ZOE 2.0") is a community-based, multi-ethnic, cross-sectional, genetic epidemiologic study seeking to address this knowledge gap. This paper describes the study's design, the cohort's demographic profile, data domains, and key oral health outcomes. Between 2016 and 2019, the study enrolled 8059 3-5-year-old children attending public preschools in North Carolina, United States. Participants resided in 86 of the state's 100 counties and racial/ethnic minorities predominated-for example, 48% (n = 3872) were African American, 22% white, and 20% (n = 1611) were Hispanic/Latino. Seventy-nine percent (n = 6404) of participants underwent clinical dental examinations yielding ECC outcome measures-ECC (defined at the established caries lesion threshold) prevalence was 54% and the mean number of decayed, missing, filled surfaces due to caries was eight. Nearly all (98%) examined children provided sufficient DNA from saliva for genotyping. The cohort's community-based nature and rich data offer excellent opportunities for addressing important clinical, epidemiologic, and biological questions in early childhood.

The building blocks of precision oral health in early childhood: the ZOE 2.0 study

Improving children's oral health is a long-standing area of priority and sustained efforts by many stakeholders. Despite these efforts, dental caries, particularly early childhood caries (ECC), persists as a clinical and dental public health problem with multilevel consequences. Despite recent successes in the non-restorative management of dental caries, remarkably little has been done in the domain of ECC prevention. There is promise and expectation that meaningful improvements in early childhood oral health and ECC prevention can be made via the advent of precision medicine in the oral health domain. We posit that precision dentistry, including genomic influences, may be best examined in the context of well-characterized communities (versus convenience clinical samples) and the impact of contextual factors including geography and social disadvantage may be explainable via mechanistic (i.e., biological) research. This notion is aligned with the population approach in precision medicine, which calls for the latter to be predictive, preventive, personalized, and participatory. The article highlights research directions that must be developed for precision dentistry and precision dental public health to be realized. In this context, we describe the rationale, activities, and early insights gained from the ZOE 2.0 study - a large-scale, community-based, genetic epidemiologic study of early childhood oral health. We anticipate that this long-term research program will illuminate foundational domains for the advancement of precision dentistry and precision dental public health. Ultimately, this new knowledge can help catalyze the development of effective preventive and therapeutic modalities via actions at the policy, community, family, and person level.

Role of diet in ECC affected South Indian children assessed by the HEI-2005: A pilot study

BACKGROUND

"Early Childhood Caries"(ECC) is a serious global oral health problem affecting children of 71 months of age or younger. ECC has a multifactorial model of causation and diet imparts an intricately specific effect.

AIM

The study aims to determine the protective and harmful role of different dietary consumption in the causation of ECC in South Indian children, assessed by the Healthy Eating Index-2005 (HEI-2005).

SETTINGS AND DESIGN

A pilot study of cross-sectional analytical study design was conducted in a dental college and hospitals in India.

MATERIALS AND METHODS

Hundred healthy South Indian children of 3-6 years age were screened for dental caries by the ICDAS II criteria, dmf/dmfs and pufa index. Participants were divided into three groups according to their caries status such as [Group 1:caries-free, group 2:ECC, group 3:severe ECC (S-ECC)]. Questionnaires were collected with demographic details, 24 h previous dietary record, and a subsequent 3-day chart of dietary consumption. Accordingly, the HEI-2005 score was calculated for each participant. Descriptive statistics was used for analysis of sociodemographic data, Kruskal-Wallis test for multivariate analysis, and for interpreting the total effect of HEI on study groups, logistic regression analysis was used.

RESULTS

Caries experience in South Indian children demonstrated a significant association with age. Caries-free children showed significantly higher association with darkgreen/orange vegetables/legumes, milk, and calories from SoFAAS (solid fat, alcohol, and added sugars) than the other groups.

CONCLUSIONS

The study findings illustrated a prominent protective role played by specific components of the HEI-2005, as healthy dietary intake against dental caries in South Indian children.

Genomics of periodontal disease and tooth morbidity

In this review we critically summarize the evidence base and the progress to date regarding the genomic basis of periodontal disease and tooth morbidity (ie, dental caries and tooth loss), and discuss future applications and research directions in the context of precision oral health and care. Evidence for these oral/dental traits from genome-wide association studies first emerged less than a decade ago. Basic and translational research activities in this domain are now under way by multiple groups around the world. Key departure points in the oral health genomics discourse are: (a) some heritable variation exists for periodontal and dental diseases; (b) the environmental component (eg, social determinants of health and behavioral risk factors) has a major influence on the population distribution but probably interacts with factors of innate susceptibility at the person-level; (c) sizeable, multi-ethnic, well-characterized samples or cohorts with high-quality measures on oral health outcomes and genomics information are required to make decisive discoveries; (d) challenges remain in the measurement of oral health and disease, with current periodontitis and dental caries traits capturing only a part of the health-disease continuum, and are little or not informed by the underlying biology; (e) the substantial individual heterogeneity that exists in the clinical presentation and lifetime trajectory of oral disease can be identified and leveraged in a precision medicine framework or, if unappreciated, can hamper translational efforts. In this review we discuss how composite or biologically informed traits may offer improvements over clinically defined ones for the genomic interrogation of oral diseases. We demonstrate the utility of the results of genome-wide association studies for the development and testing of a genetic risk score for severe periodontitis. We conclude that exciting opportunities lie ahead for improvements in the oral health of individual patients and populations via advances in our understanding of the genomic basis of oral health and disease. The pace of new discoveries and their equitable translation to practice will largely depend on investments in the education and training of the oral health care workforce, basic and population research, and sustained collaborative efforts..

Searching Deep and Wide: Advances in the Molecular Understanding of Dental Caries and Periodontal Disease

During the past decades, remarkable progress has been made in the understanding of the molecular basis of the 2 most common oral diseases, dental caries and periodontal disease. Improvements in our knowledge of the diseases' underlying biology have illuminated previously unrecognized aspects of their pathogenesis. Importantly, the key role of the oral (supragingival and subgingival) microbiome is now well recognized, and both diseases are now best understood as dysbiotic. From a host susceptibility standpoint, some progress has been made in dissecting the "hyperinflammatory" trait and other pathways of susceptibility underlying periodontitis, and novel susceptibility loci have been reported for dental caries. Nevertheless, there is a long road to the translation of these findings and the realization of precision oral health. There is promise and hope that the rapidly increasing capacity of generating multiomics data layers and the aggregation of study samples and cohorts comprising thousands of participants will accelerate the discovery and translation processes. A first key element in this process has been the identification and interrogation of biologically informed disease traits-these "deep" or "precise" traits have the potential of revealing biologically homogeneous disease signatures and genetic susceptibility loci that might present with overlapping or heterogeneous clinical signs. A second key element has been the formation of international consortia with the goals of combining and harmonizing oral health data of thousands of individuals from diverse settings-these "wide" collaborative approaches leverage the power of large sample sizes and are aimed toward the discovery or validation of genetic influences that would otherwise be impossible to detect. Importantly, advancements via these directions require an unprecedented engagement of systems biology and team science models. The article highlights novel insights into the molecular basis of dental caries and chronic periodontitis that have been gained from recent and ongoing studies involving "deep" and "wide" analytical approaches.

Pilot GWAS of caries in African-Americans shows genetic heterogeneity

BACKGROUND

Dental caries is the most common chronic disease in the US and disproportionately affects racial/ethnic minorities. Caries is heritable, and though genetic heterogeneity exists between ancestries for a substantial portion of loci associated with complex disease, a genome-wide association study (GWAS) of caries specifically in African Americans has not been performed previously.

METHODS

We performed exploratory GWAS of dental caries in 109 African American adults (age > 18) and 96 children (age 3-12) from the Center for Oral Health Research in Appalachia (COHRA1 cohort). Caries phenotypes (DMFS, DMFT, dft, and dfs indices) assessed by dental exams were tested for association with 5 million genotyped or imputed single nucleotide polymorphisms (SNPs), separately in the two age groups. The GWAS was performed using linear regression with adjustment for age, sex, and two principal components of ancestry. A maximum of 1 million adaptive permutations were run to determine empirical significance.

RESULTS

No loci met the threshold for genome-wide significance, though some of the strongest signals were near genes previously implicated in caries such as antimicrobial peptide DEFB1 (rs2515501; p = 4.54 × 10- 6) and TUFT1 (rs11805632; p = 5.15 × 10- 6). Effect estimates of lead SNPs at suggestive loci were compared between African Americans and Caucasians (adults N = 918; children N = 983). Significant (p < 5 × 10- 8) genetic heterogeneity for caries risk was found between racial groups for 50% of the suggestive loci in children, and 12-18% of the suggestive loci in adults.

CONCLUSIONS

The genetic heterogeneity results suggest that there may be differences in the contributions of genetic variants to caries across racial groups, and highlight the critical need for the inclusion of minorities in subsequent and larger genetic studies of caries in order to meet the goals of precision medicine and to reduce oral health disparities.

The Era of the Genome and Dental Medicine

Understanding the "code of life" and mapping the human genome have been monumental and era-defining scientific landmarks-analogous to setting foot on the moon. The last century has been characterized by exponential advances in our understanding of the biological and specifically molecular basis of health and disease. The early part of the 20th century was marked by fundamental theoretical and scientific advances in understanding heredity, the identification of the DNA molecule and genes, and the elucidation of the central dogma of biology. The second half was characterized by experimental and increasingly molecular investigations, including clinical and population applications. The completion of the Human Genome Project in 2003 and the continuous technological advances have democratized access to this information and the ability to generate health and disease association data; however, the realization of genomic and precision medicine, to practically improve people's health, has lagged. The oral health domain has made great strides and substantially benefited from the last century of advances in genetics and genomics. Observations regarding a hereditary component of dental caries were reported as early as the 1920s. Subsequent breakthroughs were made in the discovery of genetic causes of rare diseases, such as ectodermal dysplasias, orofacial clefts, and other craniofacial and dental anomalies. More recently, genome-wide investigations have been conducted and reported for several diseases and traits, including periodontal disease, dental caries, tooth agenesis, cancers of the head and neck, orofacial pain, temporomandibular disorders, and craniofacial morphometrics. Gene therapies and gene editing with CRISPR/Cas represent the latest frontier surpassed in the era of genomic medicine. Amid rapid genomics progress, several challenges and opportunities lie ahead. Importantly, systematic efforts supported by implementation science are needed to realize the full potential of genomics, including the improvement of public and practitioner genomics literacy, the promotion of individual and population oral health, and the reduction of disparities.

Human genes influence the interaction between Streptococcus mutans and host caries susceptibility: a genome-wide association study in children with primary dentition

Streptococcus mutans is a well-known cause of dental caries, due to its acidogenicity, aciduricity, and ability to synthesize exopolysaccharides in dental plaques. Intriguingly, not all children who carry S. mutans manifest caries, even with similar characteristics in oral hygiene, diet, and other environmental factors. This phenomenon suggests that host susceptibility potentially plays a role in the development of dental caries; however, the association between host genetics, S. mutans, and dental caries remains unclear. Therefore, this study examined the influence of host gene-by-S. mutans interaction on dental caries. Genome-wide association analyses were conducted in 709 US children (<13 years old), using the dbGap database acquired from the center for oral health research in appalachia (COHRA) and the Iowa Head Start programmes (GEIRS). A generalized estimating equation was used to examine the gene-by-S. mutans interaction effects on the outcomes (decayed and missing/filled primary teeth due to caries). Sequentially, the COHRA and GEIRS data were used to identify potential interactions and replicate the findings. Three loci at the genes interleukin 32 (IL32), galactokinase 2 (GALK2), and CUGBP, Elav-like family member 4 (CELF4) were linked to S. mutans carriage, and there was a severity of caries at a suggestive significance level among COHRA children (P < 9 × 10-5), and at a nominal significance level among GEIRS children (P = 0.047-0.001). The genetic risk score that combined the three loci also significantly interacted with S. mutans (P < 0.000 1). Functional analyses indicated that the identified genes are involved in the host immune response, galactose carbohydrate metabolism, and food-rewarding system, which could potentially be used to identify children at high risk for caries and to develop personalized caries prevention strategies.

Protocols, Methods, and Tools for Genome-Wide Association Studies (GWAS) of Dental Traits

Oral health and disease are known to be influenced by complex interactions between environmental (e.g., social and behavioral) factors and innate susceptibility. Although the exact contribution of genomics and other layers of "omics" to oral health is an area of active research, it is well established that the susceptibility to dental caries, periodontal disease, and other oral and craniofacial traits is substantially influenced by the human genome. A comprehensive understanding of these genomic factors is necessary for the realization of precision medicine in the oral health domain. To aid in this direction, the advent and increasing affordability of high-throughput genotyping has enabled the simultaneous interrogation of millions of genetic polymorphisms for association with oral and craniofacial traits. Specifically, genome-wide association studies (GWAS) of dental caries and periodontal disease have provided initial insights into novel loci and biological processes plausibly implicated in these two common, complex, biofilm-mediated diseases. This paper presents a summary of protocols, methods, tools, and pipelines for the conduct of GWAS of dental caries, periodontal disease, and related traits. The protocol begins with the consideration of different traits for both diseases and outlines procedures for genotyping, quality control, adjustment for population stratification, heritability and association analyses, annotation, reporting, and interpretation. Methods and tools available for GWAS are being constantly updated and improved; with this in mind, the presented approaches have been successfully applied in numerous GWAS and meta-analyses among tens of thousands of individuals, including dental traits such as dental caries and periodontal disease. As such, they can serve as a guide or template for future genomic investigations of these and other traits.

Measurement of Early Childhood Oral Health for Research Purposes: Dental Caries Experience and Developmental Defects of the Enamel in the Primary Dentition

Epidemiological investigations of early childhood oral health rely upon the collection of high-quality clinical measures of health and disease. However, ascertainment of valid and accurate clinical measures presents unique challenges among young, preschool-age children. The paper presents a clinical research protocol for the conduct of oral epidemiological examinations among children, implemented in ZOE 2.0, a large-scale population-based genetic epidemiologic study of early childhood caries (ECC). The protocol has been developed for the collection of information on tooth surface-level dental caries experience and tooth-level developmental defects of the enamel in the primary dentition. Dental caries experience is recorded using visual criteria modified from the International Caries Detection and Assessment System (ICDAS), and measurement of developmental defects is based upon the modified Clarkson and O'Mullane Developmental Defects of the Enamel Index. After a dental prophylaxis (toothbrushing among all children and flossing as needed), children's teeth are examined by trained and calibrated examiners in community locations, using portable dental equipment, compressed air, and uniform artificial light and magnification conditions. Data are entered directly onto a computer using a custom Microsoft Access-based data entry application. The ZOE 2.0 clinical protocol has been implemented successfully for the conduct of over 6000 research examinations to date, contributing phenotype data to downstream genomics and other "omics" studies of ECC and DDE, as well as traditional clinical and epidemiologic dental research.

The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome

Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.

Exploring the genomic basis of early childhood caries: a pilot study

OBJECTIVE

A genetic component in early childhood caries (ECC) is theorized, but no genome-wide investigations of ECC have been conducted. This pilot study is part of a long-term research program aimed to: (1) determine the proportion of ECC variance attributable to the human genome and (2) identify ECC-associated genetic loci.

METHODS

The study's community-based sample comprised 212 children (mean age=39 months; range = 30-52 months; males = 55%; Hispanic/Latino = 35%, African-American = 32%; American Academy of Pediatric Dentistry definition of ECC prevalence = 38%). Approximately 2.4 million single nucleotide polymorphisms (SNPs) were genotyped using DNA purified from saliva. A P < 5 × 10^-8 criterion was used for genome-wide significance. SNPs with P < 5 × 10^-5 were followed-up in three independent cohorts of 921 preschool-age children with similar ECC prevalence.

RESULTS

SNPs with minor allele frequency ≥5% explained 52% (standard error = 54%) of ECC variance (one-sided P = 0.03). Unsurprisingly, given the pilot's small sample size, no genome-wide significant associations were found. An intergenic locus on 4q32 (rs4690994) displayed the strongest association with ECC [P = 2.3 × 10^-6 ; odds ratio (OR) = 3.5; 95% confidence interval (CI) = 2.1-5.9]. Thirteen loci with suggestive associations were followed-up - none showed evidence of association in the replication samples.

CONCLUSION

This study's findings support a heritable component of ECC and demonstrate the feasibility of conducting genomics studies among preschool-age children.