Table 3.
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) | |||
Highd orange complex colonization | 978 | |||
+ 10 PCs for population structure | 0.464 (0.32) | 0.318 (0.30) | ||
+ 10 PCs, sex, age | 0.456 (0.32) | 0.310 (0.29) | ||
Highd red complex colonization | 986 | |||
+ 10 PCs for population structure | 0.565 (0.31) | 0.424 (0.29) | ||
+ 10 PCs, sex, age | 0.534 (0.31) | 0.405 (0.29) | ||
Highe GCF IL-1β expression | 4,907 | |||
+ 10 PCs for population structure | 0.156 (0.08) | 0.155 (0.08) | ||
+ 10 PCs, sex, age | 0.155 (0.08) | 0.156 (0.08) | ||
PCTf1 | 975 | |||
+ 10 PCs for population structure | <0.0001 | <0.0001 | ||
+ 10 PCs, sex, age | <0.0001 | <0.0001 | ||
PCTf2 | 975 | |||
+ 10 PCs for population structure | 0.18 (0.36) | 0.01 (0.31) | ||
+ 10 PCs, sex, age | 0.14 (0.36) | <0.0001 | ||
PCTf3 | 975 | |||
+ 10 PCs for population structure | 0.71 (0.32) | 0.57 (0.30) | ||
+ 10 PCs, sex, age | 0.72 (0.32) | 0.57 (0.31) | ||
PCTf4 | 975 | |||
+ 10 PCs for population structure | <0.0001 | <0.0001 | ||
+ 10 PCs, sex, age | <0.0001 | <0.0001 | ||
PCTf5 | 975 | |||
+ 10 PCs for population structure | 0.16 (0.35) | 0.15 (0.31) | ||
+ 10 PCs, sex, age | 0.18 (0.35) | 0.17 (0.31) | ||
PCTf6 | 975 | |||
+ 10 PCs for population structure | 0.19 (0.36) | 0.19 (0.31) | ||
+ 10 PCs, sex, age | 0.40 (0.35) | 0.35 (0.31) |
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
Defined as the highest quintile versus the lower 4 quintiles, as quantitated by checkerboard DNA-DNA hybridization (Divaris et al. 2012)
Defined as the top quartile versus the lower 3 quartiles (Offenbacher et al. 2018)
Periodontal complex trait, introduced by Offenbacher et al. 2016