Table 2.
Genotyped SNPs | Imputeda SNPs | |||
---|---|---|---|---|
Exclusion filters: | MAF < 0.05 | MAF < 0.05, R2(b) < 0.6 | ||
n (SNPs)c: | n | 656,292 | 2,104,905 | |
variance explained (se) | variance explained (se) | |||
any PPCd (disease) vs. healthy | 4,504 | |||
+ 10 PCs for population structure | 0.084 (0.07) | 0.064 (0.06) | ||
+ 10 PCs, sex, age | 0.073 (0.07) | 0.056 (0.06) | ||
PPCd: “high gingival index” vs. healthy | 1,621 | |||
+ 10 PCs for population structure | 0.479 (0.19) | 0.397 (0.17) | ||
+ 10 PCs, sex, age | 0.517 (0.19) | 0.454 (0.17) | ||
PPCd: “posterior disease”, “severe disease”, “tooth loss”, “severe tooth loss” vs. healthy | 3,532 | |||
+ 10 PCs for population structure | 0.041 (0.09) | 0.046 (0.08) | ||
+ 10 PCs, sex, age | 0.038 (0.09) | 0.047 (0.08) | ||
PPCd: “posterior disease”, “severe disease”, “tooth loss”, “severe tooth loss” vs. healthy | 2,705 | |||
+ 10 PCs for population structure | 0.155 (0.12) | 0.120 (0.10) | ||
+ 10 PCs, sex, age | 0.149 (0.12) | 0.126 (0.10) | ||
PPCd: “severe disease” vs. healthy | 1,699 | |||
+ 10 PCs for population structure | 0.272 (0.19) | 0.158 (0.17) | ||
+ 10 PCs, sex, age | 0.257 (0.19) | 0.142 (0.17) | ||
PPCd: “severe disease”, “severe tooth loss” vs. healthy | 2,174 | |||
+ 10 PCs for population structure | 0.245 (0.15) | 0.152 (0.13) | ||
+ 10 PCs, sex, age | 0.261 (0.15) | 0.171 (0.13) | ||
PPCd: “tooth loss”, “severe tooth loss” vs. healthy | 2,467 | |||
+ 10 PCs for population structure | 0.103 (0.13) | 0.079 (0.11) | ||
+ 10 PCs, sex, age | 0.106 (0.13) | 0.096 (0.11) | ||
Periodontitis WW17e Stage 3 vs. 1/2 | 3,414 | |||
+ 10 PCs for population structure | 0.062 (0.10) | 0.108 (0.08) | ||
+ 10 PCs, sex, age | 0.076 (0.10) | 0.123 (0.08) | ||
Periodontitis WW17e Stage 3/4 vs. 1/2 | 3,047 | |||
+ 10 PCs for population structure | 0.079 (0.07) | 0.103 (0.06) | ||
+ 10 PCs, sex, age | 0.084 (0.07) | 0.116 (0.06) | ||
Periodontitis WW17e Stage 4 vs. 1/2 | 4,504 | |||
+ 10 PCs for population structure | 0.175 (0.11) | 0.139 (0.09) | ||
+ 10 PCs, sex, age | 0.146 (0.11) | 0.125 (0.09) |
MAF, minor allele frequency; se, standard error; PCs, principal components
Imputed using HapMap II-CEU
Imputation quality score
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
Periodontal profile class, introduced by Morelli et al. 2016
2017 world workshop on the classification of periodontal and peri-implant diseases and conditions (Papapanou et al. 2018)