Table 1.
Phenotypic variance explained for ‘traditional’, clinically-defined oral and dental traits by all genotyped and imputed autosomal SNPs available among the European American participants of the Dental Atherosclerosis Risk In Communities study (n = 4,504).
| Genotyped SNPs | Imputeda SNPs | |||
|---|---|---|---|---|
| Exclusion filters: | MAF < 0.05 | MAF < 0.05, R2(b) < 0.6 | ||
| n (SNPs)c: | 656,292 | 2,104,905 | ||
| variance explained (se) | variance explained (se) | |||
| Number of remaining teeth | ||||
| + 10 PCs for population structure | 0.115 (0.07) | 0.065 (0.06) | ||
| + 10 PCs, sex, age | 0.114 (0.07) | 0.064 (0.06) | ||
| Incident Tooth Lossd | ||||
| + 10 PCs for population structure | 0.064 (0.11) | 0.006 (0.09) | ||
| + 10 PCs, sex, age | 0.055 (0.11) | 0.001 (0.10) | ||
| DMFS (decayed, missing, filled tooth surfaces due to caries) | ||||
| + 10 PCs for population structure | 0.126 (0.08) | 0.057 (0.06) | ||
| + 10 PCs, sex, age | 0.131 (0.08) | 0.066 (0.06) | ||
| Tooth morbidity (DMFS including teeth lost due to all causes) | ||||
| + 10 PCs for population structure | 0.256 (0.07) | 0.184 (0.06) | ||
| + 10 PCs, sex, age | 0.242 (0.07) | 0.171 (0.06) | ||
| Any periodontitis (moderate/severe versus health/mild) | ||||
| + 10 PCs for population structure | 0.012 (0.07) | 0.039 (0.06) | ||
| + 10 PCs, sex, age | 0.018 (0.08) | 0.049 (0.06) | ||
| Moderate periodontitis (versus health/mild) | ||||
| + 10 PCs for population structure | 0.006 (0.14) | 0.068 (0.12) | ||
| + 10 PCs, sex, age | 0.000 (0.14) | 0.066 (0.12) | ||
| Severe periodontitis (versus health/mild) | ||||
| + 10 PCs for population structure | 0.175 (0.19) | 0.083 (0.16) | ||
| + 10 PCs, sex, age | 0.220 (0.19) | 0.127 (0.16) | ||
| Mean interproximal attachment loss | ||||
| + 10 PCs for population structure | 0.161 (0.07) | 0.122 (0.06) | ||
| + 10 PCs, sex, age | 0.152 (0.08) | 0.106 (0.06) | ||
| Extent of attachment loss ≥ 3mm (proportion of sites) | ||||
| + 10 PCs for population structure | 0.113 (0.08) | 0.073 (0.06) | ||
| + 10 PCs, sex, age | 0.075 (0.08) | 0.037 (0.06) | ||
| Extent of attachment loss ≥ 4mm (proportion of sites) | ||||
| + 10 PCs for population structure | 0.092 (0.07) | 0.053 (0.06) | ||
| + 10 PCs, sex, age | 0.076 (0.07) | 0.035 (0.06) | ||
| Extent of probing depth ≥ 4mm (proportion of sites) | ||||
| + 10 PCs for population structure | 0.167 (0.07) | 0.143 (0.06) | ||
| + 10 PCs, sex, age | 0.190 (0.07) | 0.150 (0.06) |
MAF, minor allele frequency; se, standard error; PCs, principal components
a
Imputed using HapMap II-CEU
b
Imputation quality score
c
Number of SNPs that were used to estimate the genetic relationship matrix after exclusions, among the study participants as a first step in the GCTA prior to conducting REML
d
Incident tooth loss was derived from a follow-up telephone survey in a subset of participants (n = 2,771) and defined as >2 teeth lost during the last decade