Table 3.

Phenotypic variance explained for 2 bacterial colonization and 6 biologically informed complex periodontal traits (PCT) 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)
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

^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

^dDefined as the highest quintile versus the lower 4 quintiles, as quantitated by checkerboard DNA-DNA hybridization (Divaris et al. 2012)

^eDefined as the top quartile versus the lower 3 quartiles (Offenbacher et al. 2018)

^fPeriodontal complex trait, introduced by Offenbacher et al. 2016