title: Heritable patterns of tooth decay in the permanent dentition: principal components and factor analyses.
abstract: BACKGROUND
  Dental caries is the result of a complex interplay among environmental, behavioral, and genetic factors, with distinct patterns of decay likely due to specific etiologies. Therefore, global measures of decay, such as the DMFS index, may not be optimal for identifying risk factors that manifest as specific decay patterns, especially if the risk factors such as genetic susceptibility loci have small individual effects. We used two methods to extract patterns of decay from surface-level caries data in order to generate novel phenotypes with which to explore the genetic regulation of caries.
  
  
  METHODS
  The 128 tooth surfaces of the permanent dentition were scored as carious or not by intra-oral examination for 1,068 participants aged 18 to 75 years from 664 biological families. Principal components analysis (PCA) and factor analysis (FA), two methods of identifying underlying patterns without a priori surface classifications, were applied to our data.
  
  
  RESULTS
  The three strongest caries patterns identified by PCA recaptured variation represented by DMFS index (correlation, r = 0.97), pit and fissure surface caries (r = 0.95), and smooth surface caries (r = 0.89). However, together, these three patterns explained only 37% of the variability in the data, indicating that a priori caries measures are insufficient for fully quantifying caries variation. In comparison, the first pattern identified by FA was strongly correlated with pit and fissure surface caries (r = 0.81), but other identified patterns, including a second pattern representing caries of the maxillary incisors, were not representative of any previously defined caries indices. Some patterns identified by PCA and FA were heritable (h(2) = 30-65%, p = 0.043-0.006), whereas other patterns were not, indicating both genetic and non-genetic etiologies of individual decay patterns.
  
  
  CONCLUSIONS
  This study demonstrates the use of decay patterns as novel phenotypes to assist in understanding the multifactorial nature of dental caries.
authors.affiliation: Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA. jrs51@pitt.edu
authors.forename: John R
authors.initials: JR
authors.lastname: Shaffer
authors.forename: Eleanor
authors.initials: E
authors.lastname: Feingold
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Wang
authors.forename: Karen T
authors.initials: KT
authors.lastname: Tcuenco
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Weeks
authors.forename: Rebecca S
authors.initials: RS
authors.lastname: DeSensi
authors.forename: Deborah E
authors.initials: DE
authors.lastname: Polk
authors.forename: Steve
authors.initials: S
authors.lastname: Wendell
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Weyant
authors.forename: Richard
authors.initials: R
authors.lastname: Crout
authors.forename: Daniel W
authors.initials: DW
authors.lastname: McNeil
authors.forename: Mary L
authors.initials: ML
authors.lastname: Marazita
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D001061:Appalachian Region / Q000453:epidemiology; D004245:DMF Index; D003731:Dental Caries / Q000453:epidemiology / Q000235:genetics* / Q000473:pathology*; D003733:Dental Caries Susceptibility / Q000235:genetics*; D003750:Dental Fissures / Q000235:genetics / Q000473:pathology; D019229:Dentition, Permanent; D005163:Factor Analysis, Statistical; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006801:Humans; D008875:Middle Aged; D020412:Multifactorial Inheritance; D010641:Phenotype; D015995:Prevalence; D025341:Principal Component Analysis; D055815:Young Adult