Center for Oral Health Research in Appalachia (COHRA) Genomic Studies of Oral Health and Disease

The purpose of this project is to identify the genetic factors contributing to dental caries in children and adults. The datasets come from the Center for Oral Health Research in Appalachia (COHRA), which has the long-term goal of determining the sources of oral health disparities in a high risk, Northern Appalachian population so that effective preventive interventions can be designed and targeted. The Specific Aims of this project are to perform genome-wide association scans of dental caries of the (1) primary dentition in children, and (2) permanent dentition in adults, to identify novel risk variants and to replicate previously nominated risk variants. This project brings together samples from three cohorts: COHRA1 is a cross-sectional cohort comprising members of 862 northern Appalachian families; approximately 80% of the cohort has been previously genotyped by the Center for Inherited Disease Research with support from NIDCR using the Illumina Quad W array (see dbGaP Study Accession: phs000095.v3.p1). Dental SCORE is a cross-sectional cohort comprising approximately 550 unrelated individuals who underwent the same data collection protocol as COHRA1. COHRA2 is an ongoing longitudinal cohort that recruited approximately 1100 northern Appalachian women during pregnancy, and followed them and their children through their children's early childhood; the current project period will continue data collect though age 6 of the child.

Phenotypes for this project were derived from intra-oral examinations performed by trained and calibrated research hygienists. In brief, each tooth was recorded as present or absent, and each surface of each present tooth was scored for evidence of decay. From these data, dental caries indices were generated. This project contains two phases of genotyping: (1) collection of exome SNP Chip data for the previously genotyped COHRA1 samples, and (2) collection of whole-genome SNP Chip data for the remaining COHRA1 samples and all Dental SCORE and COHRA2 samples.

These data will support efforts to test hypotheses regarding the causal relationships of risk factors contributing to the unusually high rates of caries formation in the Appalachian population. Ultimately, these data may inform the development of an integrated model of caries risk, in which the effects of genetics, oral ecology, diet, and other environmental/psychosocial factors and behaviors are modeled in concert to explain the disparities, including the high rate of caries onset before age 6. The gene-mapping Aims of this project, which seek to identify the genetic factors that contribute to caries risk, are a requisite step in realizing this integrated model.

• Study Weblinks:
  • Oral Health Studies
• Study Design:
  • Family/Twin/Trios
• Study Type:
  • Cohort
  • Family
  • Longitudinal Cohort
• dbGaP estimated ancestry using GRAF-pop
• Total number of consented subjects: 5210
• Subject Sample Telemetry Report (SSTR)

• BioProject
• PubMed
• PMC

COHRA1: Inclusion criteria included households with one biological parent-child pair living together with the child being between ages 1 and 18 years; all members of eligible households were offered admission into the study regardless of biological or legal relationships and regardless of oral health conditions. Exclusion criteria included individuals with neurological impairment, physical or intellectual handicap, or psychosis, and households for which the adult or child of the biological parent-child pair had either a reduced capacity to resist infection or form blood clots due to reasons such as leukemia, cancer, unstable diabetes, transplant, blood clotting disorder, corticosteroid use, immunosuppressive therapy, blood thinning medications, or HIV.

COHRA2: Inclusion criteria included pregnant Caucasian women between the 12th and 29th weeks of pregnancy who were at least 18 years of age and fluent in English. Exclusion criteria included women who were carrying a multiple pregnancy, had tuberculosis, were immunocompromised, or did not have telephone. Additionally, women were excluded based on pregnancy outcomes such as premature delivery or development of serious medical issues in the mother or baby.

Dental SCORE: Participants enrolled in the Heart SCORE study were eligible to participate in this ancillary study. Heart SCORE inclusion criteria required adult participants to be ages 45 to 75 years. Exclusion criteria included pregnancy and comorbidities that limited life expectancy to less than 5 years.

1999: Center for Oral Health Research in Appalachia (COHRA) was established as a consortium between the University of Pittsburgh and West Virginia University to address oral health disparities in rural Appalachia.
2003: Recruitment for the COHRA1 family-based sample was initiated in West Virginia.
2004: Recruitment for the COHRA1 family-based sample was initiated in Pennsylvania.
2007: Recruitment for the Dental SCORE sample was initiated in Pittsburgh, Pennsylvania.
2009: Genotyping was performed for approximately 80% of the COHRA1 sample by the Center for Inherited Disease Research (CIDR) at Johns Hopkins University.
2011: Recruitment for the COHRA2 mother-baby sample was initiated in West Virginia. Three in-person assessments took place during the first year of participation including a prenatal visit (12-29 weeks of pregnancy), pre-tooth visit (baby age 2-3 months), and 1-year visit. Annual in-person visits took place at child ages 2 to 6 years. Telephone interviews occurred once prenatally, and postnatally at baby ages 10 weeks and 6 months, and every 6 months thereafter.
2012: Recruitment for the COHRA2 mother-baby sample was initiated in Pittsburgh, Pennsylvania. Longitudinal assessments took place as in West Virginia with two additional in-person visits occurring at birth and one month after the eruption of the baby's first tooth.
2017: New recruitment for the COHRA2 sample closed; longitudinal follow-up continued.
2018: Genotyping of COHRA1, Dental SCORE, and COHRA2 for the current project performed by the Center for Inherited Disease Research (CIDR) of Johns Hopkins University.

• Primary Phenotype: Dental Caries

• Principal Investigator
  • John R. Shaffer, PhD. University of Pittsburgh, Pittsburgh, PA, USA.
  • Eleanor Feingold, PhD. University of Pittsburgh, Pittsburgh, PA, USA.
• Co-Investigators
  • Mary L. Marazita, PhD. University of Pittsburgh, Pittsburgh, PA, USA.
• Co-Investigator
  • Daniel W. McNeil, PhD. West Virginia University, Morgantown, WV, USA.
  • Robert J. Weyant, MS, DMD, DrPH. University of Pittsburgh, Pittsburgh, PA, USA.
  • Betsy Foxman, PhD. University of Michigan, Ann Arbor, MI, USA.
• Funding Source
  • R01-DE014899. National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
  • X01-HG009878. National Human Genome Research Institute, CIDR genotyping, National Institutes of Health, Bethesda, MD, USA.