Table 2.

Phenotypic variance explained for contemporary classifications of periodontitis by all genotyped and imputed autosomal SNPs available among European American participants of the Dental Atherosclerosis Risk In Communities study.

		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

^aImputed using HapMap II-CEU

^bImputation quality score

^cNumber 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

^dPeriodontal profile class, introduced by Morelli et al. 2016

^e2017 world workshop on the classification of periodontal and peri-implant diseases and conditions (Papapanou et al. 2018)