Dental Caries: Whole Genome Association and Gene x Environment Studies

Dental caries (also known as tooth decay) remains the most common chronic disease of childhood, five times more common than asthma and seven times more common than environmental allergies, with more than 40% of children exhibiting caries when they enter kindergarten. In 2005, it was estimated that dental health care costs were approximately $84 billion, of which 60% or about $50 billion were related to treatment of dental caries. Although overall caries prevalence has declined over the last 40 years, dental caries in the primary dentition and mean caries rates in children ages 2-11 has increased markedly over the past 12 years. Childhood caries is a serious public health issue because of associated health problems and because disparities in oral health have led to substantially higher average disease prevalence among children in poverty and in under-served racial and ethnic groups. These issues are of such concern that in 2005, the American Academy of Pediatrics made children's oral health one of their top areas of focus, as it is for the majority of the NIDCR "Disparities Centers".

The etiology of dental caries has been studied for many years. Multiple factors contribute to a person's risk for caries, including: 1) environmental factors such as diet, oral hygiene, fluoride exposure and the level of colonization of cariogenic bacteria and 2) host factors such as salivary flow, salivary buffering capacity, position of teeth relative to each other, surface characteristics of tooth enamel and depth of occlusal fissures on posterior teeth. In spite of all that is known about this disease, there are still individuals who appear to be more susceptible to caries and those who are extremely resistant, regardless of the environmental risk factors to which they are exposed, implying that genetic factors also play an important role in caries etiology. This conclusion is supported by studies in both humans and animals, with the most compelling evidence coming from studies of twins reared apart in which investigators found significant resemblance within monozygotic (MZ) but not dizygotic (DZ) twin pairs for percentage of teeth and surfaces restored or carious and estimated the genetic contribution to caries as 40%. Other recent studies of twins reared together estimated the heritability for caries, adjusted for age and gender, as ranging from 45-64%.

Despite the strong evidence of a genetic component to risk for dental caries, there have been only a few studies of candidate genes in caries, and no published genome-wide scans. A comprehensive genome wide search is the only approach that will allow us to identify those genetic regions likely to harbor genes increasing the risk for dental caries, and eventually to identify the etiologic genes and to explore the interaction of those genes with microbiological, dietary, fluoride, and behavioral factors that are known to be associated with caries risk and progression. Therefore, the goal of this study is to perform genome-wide association (GWA) studies of dental caries with a large panel of SNP's (610,000) in families and individuals ascertained through multiple US sites (University of Pittsburgh and University of Iowa).

The v2 release of this study includes 96 additional individuals who were genotyped with the CCDG: Dental Caries and CL/P in Guatemala project (dbGaP accession number phs000440) to augment the data initially presented here. These subjects were genotyped on the Illumina 610 platform to make their data comparable.

This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org), which was developed through the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to dental caries through large-scale genome-wide association studies of well-characterized families and individuals at multiple sites in the U.S. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). The study was supported by the National Institute of Dental and Craniofacial Research (NIDCR, U01-DE018903). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.

Samples of some participants in this study were selected for further genomic analysis. These results will be available in the dbGaP CIDR study: Center for Oral Health Research in Appalachia (COHRA) Genomic Studies of Oral Health and Disease (phs001591).

• Study Design:
  • Family/Twin/Trios
• Study Type:
  • Nuclear Families
  • Parent-Offspring Trios
  • Case-Control
• dbGaP estimated ancestry using GRAF-pop
• Total number of consented subjects: 5417
• Subject Sample Telemetry Report (SSTR)

• BioSample

Population-based ascertainment, followed by dental exams. Dental caries has a range of expressions.

There are four sites in the study (abbreviated PITT, DRDR, IOWA and GEIRS), from two Universities (Pittsburgh and Iowa):

University of Pittsburgh - History: The two University of Pittsburgh sites are PITT and DRDR.

PITT site: The families from the PITT site were ascertained through the Center for Oral Health Research in Appalachia (COHRA) under the leadership of Dr. Mary L. Marazita. COHRA was established in 1999 as a consortium between the University of Pittsburgh and West Virginia University in response to the persistent and overwhelming oral health disparity found among the rural Appalachian population. Rural Appalachian disease patterns are characterized by early and significant onset of caries and/or periodontal disease, often leading to early tooth loss and ultimately culminating in complete edentulism by young adulthood. Recruitment for the study began in 2003. COHRA is funded by NIH/NIDCR (1R01-DE014899, "Genetic Factors Contributing to Oral Health Disparities in Appalachia"; R01-DE 014889-03S1, "Psychosocial Influences on Rural Children's Oral Health"; R01-DE 014889-04S1, "Oral Microbiology Studies in Appalachia"; and 2R01-DE013899, "Factors Contributing to Oral Health Disparities in Appalachia"), and relies heavily on Community Advisory Boards composed of local residents to guide investigation in a manner that is culturally appropriate and addresses perceived needs of the community.

The study sample is drawn from four rural Appalachian counties (two in West Virginia and two in Pennsylvania), and an urban sample in the Appalachian region. In order to participate in the COHRA study, a family must have at least one adult and at least one biological child of that adult (all family members resident in the same household must participate in order for a family to be "complete").

Participants receive a comprehensive orodental examination every two years conducted by a licensed dentist or dental hygienist in a well equipped, modern dental operatory. Data for each study participant, includes height, weight, body mass, orodental status and history, medical history, health behaviors, parental and family level variables, social adjustment, demographics (ethnicity, SES, etc), dental fear, fatalism, health attitudes, DNA source (blood, saliva), saliva, microbiological samples and assessments of bacteria (including S. mutans), water samples and fluoride assessments.

DRDR site: The University of Pittsburgh School of Dental Medicine (SDM) instituted the Dental Registry and DNA Repository (DRDR) in 2008 under Dr. Alexandre Vieira as director. All individuals seeking treatment at the SDM are invited to be part of the program and to give permission to have the information on their dental chart be used for future research related to dental and craniofacial conditions, and provide a saliva sample for DNA analysis. Data in the DRDR include all the data in the SDM dental record (demographic, dental exams, tests including S mutans, diagnostic Xrays). DRDR is partially funded by the support from the University of Pittsburgh Clinical and Translational Science Institute (NIH/NCRR/CTSA grant number UL1-RR024153) and partially through SDM internal funding.

University of Iowa - History: The two University of Iowa sites are IOWA and GEIRS.

IOWA: The study families from the IOWA site were ascertained from one study time point of two related longitudinal studies, the Iowa Fluoride Study and the Iowa Bone Development Study under the leadership of Dr. Steven Levy.

The Iowa Fluoride Study (IFS) is a longitudinal study of children designed to quantify fluoride exposures from both dietary and non-dietary sources and to associate longitudinal fluoride exposures with dental fluorosis (spots on teeth) and dental caries (cavities). Mothers of newborns were recruited from 8 Iowa hospital postpartum units between 1992 and 1995. These hospitals were responsible for the large majority of all births in the area that they served, with a combined total of about 8,000 births per the Iowa Fluoride Study and the Iowa Bone Development Study, funded by NIDCR R01-DE09551 and R01-DE12101 year, or approximately 20 percent of all births in Iowa.

At recruitment, detailed information was obtained on items of interest such as demographics, water sources, and infant feeding plans. Thereafter, questionnaires were mailed to the participants' homes at scheduled intervals (every few months) and parents provided information about the children's water sources, beverage and selected food intake, use of dietary fluoride supplements, and tooth brushing habits. Approximately 50 percent of those invited to participate elected to do so. Overall, 1,368 mothers participated in some portion of the IFS, and approximately 700 children continue to be followed at 13 to 16 years of age.

Dental examinations were conducted by trained dentist examiners to assess dental fluorosis and caries in the primary (baby) teeth at the ages of 4 to 6. The teeth were examined again at ages 8 to 10 for any remaining primary teeth and early-erupting permanent teeth. We are currently close to completing dental examinations at age 13 to assess the full permanent dentition (other than third molars which do not usually come in until about 17 years old). In addition to overall tooth health, the study is looking at the relationships between children's sucking on pacifiers and fingers over time and malocclusion. IFS was funded by R01-DE09551.

The Iowa Bone Development Study (IBDS) was initiated in 1998 and involves children and their parents from families previously participating in the Iowa Fluoride Study (see above section) at that time. The study is assessing children's bone development over time through special, low radiation x-ray type procedures and relating the findings to detailed assessments of genetic, dietary (including fluoride and calcium), physical activity, anthropometric (height, weight, etc.), demographic, and parental factors.

DNA samples were obtained beginning in 1998 within the IBDS for bone study linkage only. In the last several years, additional consent has been obtained from the majority of study subjects/families to allow children's/parents' genetic samples to be used by our study team in analyses related to dental outcomes, including dental caries and fluorosis. IBDS was funded by R01-DE12101.

GEIRS: The study population of the GEIRS site was recruited by Dr. Rebecca Slayton primarily from Iowa Head Start programs. Subject ascertainment, collection of samples and analysis of candidate genes was initiated with pilot project funding from the Comprehensive Program to Investigate Craniofacial and Dental Anomalies (P60-DE-13076) and from the Oral Health Research Clinical Core Center (P30 DE10126) at the University of Iowa. Eligible children were three to five-years-of-age and enrolled in Head Start, a federally funded child development program for low income children. For each participant, dental examinations were conducted, DNA samples from buccal brushes, microbiological assays (for S mutans and Lactobacillus). Funding for the GEIRS site was provided by P60-DE013076 and P30-DE010126.

• Primary Phenotype: Dental Caries

• Principal Investigator
  • Dr. Mary L. Marazita. University of Pittsburgh, Pittsburgh, PA, USA.
• Co-Investigators
  • Dr. Robert J. Weyant. University of Pittsburgh, Pittsburgh, PA, USA.
  • Dr. Eleanor Feingold. University of Pittsburgh, Pittsburgh, PA, USA.
  • Dr. Daniel Weeks. University of Pittsburgh, Pittsburgh, PA, USA.
  • Dr. Rich Crout. West Virginia University, Morgantown, WV, USA.
  • Dr. Daniel McNeil. West Virginia University, Morgantown, WV, USA.
  • Dr. Steven Levy. University of Iowa, Iowa City, IA, USA.
  • Dr. Marcia Willing. University of Iowa, Iowa City, IA, USA.
  • Dr. Teresa Marshall. University of Iowa, Iowa City, IA, USA.
  • Dr. Rebecca Slayton. University of Iowa, Iowa City, IA, USA.
• Genotyping Center
  • Johns Hopkins University Center for Inherited Disease Research (CIDR), Baltimore, MD, USA.
• Funding Source for Genotyping
  • HHSN268200782096C. "NIH contract High throughput genotyping for studying the genetic contributions to human disease". National Institutes of Health, Bethesda, MD, USA.
  • HHSN268201100011I. "NIH contract High throughput genotyping for studying the genetic contributions to human disease". National Institutes of Health, Bethesda, MD, USA.