AIM:To identify loci associated with chronic periodontitis through a genome-wide association study (GWAS). MATERIALS AND METHODS:A GWAS was performed in 4032 individuals of two independent cross-sectional studies of West Pomerania (SHIP n = 3365 and SHIP-TREND n = 667) with different periodontal case definitions. Samples were genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0 or the Illumina Human Omni 2.5 array. Imputation of the HapMap as well as the 1000 Genome-based autosomal and X-chromosomal genotypes and short insertions and deletions (INDELs) was performed in both cohorts. Finally, more than 17 million SNPs and short INDELs were analysed. RESULTS:No genome-wide significant associations were found for any periodontitis case definition, regardless of whether individuals aged >60 years where excluded or not. Despite no single SNP association reached genome-wide significance, the proportion of variance explained by additive effects of all common SNPs was around 23% for mean proximal attachment loss. Excluding subjects aged >60 years increased the explained variance to 34%. CONCLUSIONS:No single SNPs were found to be genome-wide significantly associated with chronic periodontitis in this study.
KEYWORDS: Study of Health in Pomerania, attachment loss, genome-wide association studies, periodontitis
PDCD6IP, ST20-MTHFS, CDH13, LOC101927025, LOC101927661, LOC101928114, LOC101928134, LOC102724761, MTHFS, CHD1, PTPRT, GPN1, C1orf87, WDR36, NRSN1, PSMA8, ZNF524, CCDC13, NKAIN2, FAM47A, ZNF579, PARP15, DEFA1, C10orf91, ADAMTS15, ABCA1, EPHA3, ETS2, NLGN1, DKK1, KDM4B, NPAP1, FRG1, ERC2, DAOA, LINC00907, SUMF1, NKAIN3, GRIK1, LRP12, HLA-DOA, FOXA1, BIRC5, C12orf74, HMX3, IGF2R, IGL, KCNJ16, FAM180A, LBP, ST20, LOC400867, NPM1P2, FAM135B, PIK3C3, LRP1B, ETAA1, RBFOX1, PGPEP1, ETNK2, NMUR2, RGMA, ERGIC1, PTEN, SEMA6A, RIT2, ROBO2, RYR3, BCORL1, SCN2A, BLK, SETMAR, CSMD1, MFSD1, SMURF2, PRB2, SNRPN, SNTB1, SS18, TGIF1, TIMP2, ROCK1P1, VPREB1, ZNF385D, THSD4, CAMK4, LINC00208, RAB6C, FAM126A, FIZ1, WDR73, ITGA8, ACTN1, ACTN2, MBD2, HS6ST2, IQSEC1