Table 2.
Chronic periodontitis GWAS loci and candidate genes from previous studies
| Gene symbola | 450 K probes b | SNPs | Functional association with periodontitis or other diseases | References |
|---|---|---|---|---|
| NIN | 2 | rs12883458 | Genome-wide significant association with severe chronic periodontitis | Rhodin et al. [1] |
| ABHD12B | 2 | rs12883458 | ||
| WHAMM | 9 | rs2890313 | ||
| KCNK1 | 0 | rs11800854 | Genome-wide significant association with red complex high colonization | |
| DAB2IP | 0 | rs10760187 | Genome-wide significant association with Porphyromonas gingivalis high colonization | |
| CLEC19A | 1 | rs1156327 | Genome-wide significant association with PCT1 (microbial community structure that has a high correlation and positive loading with all pathogens) | Offenbacher et al. [2] |
| TRA | 0 | rs3811273 | ||
| TM9SF2P | 1 | rs9557237 | ||
| GGTA2P | 0 | rs17184007 | ||
| IFI16 | 1 | rs1633266 | ||
| RBMS3 | 0 | rs17718700 | ||
| C1QTNF7 | 0 | rs4074082 | Genome-wide significant association with PCT3 (high positive loading of GCF-IL-1β and Aggregatibacter actinomycetemcomitans) | |
| TSNARE | 1 | rs9772881 | ||
| HPVC1 | 0 | rs10232172 | Genome-wide significant association with PCT4 (mixed-infection community with high positive loading of GCF-IL1, weak positive loadings of Pn, Pi, and Td, and low levels of Aa) | |
| SLC15A4 | 1 | rs7135417 | Genome-wide significant association with PCT5 (chronic periodontitis) | |
| PKP2 | 2 | rs6488099 | ||
| SNRPN | 9 | rs904310 | ||
| IL8 | 3 | Regulation of innate and acquired immune response Increased in gingival crevicular fluid from patients with periodontitis |
Zhan et al. [11] | |
| CD44 | 34 | Smoking-induced periodontal tissue destruction | ||
| CXCL1 | 7 | Stimulation of lipopolysaccharide in oral fibroblasts which leads to development of periodontal inflammation | ||
| IL6ST | 17 | Signal transducer for the interleukin family; regulates osteoclasts and calcium homeostasis | ||
| CCR1 | 11 | Trigger of bone resorption process | ||
| MMP7 | 7 | Innate host defense in periodontal tissues | ||
| MMP13 | 10 | Immunoreactivity in gingival crevicular fluid | ||
| MMP3 | 12 | Physiological tissue remodeling of periodontal tissue | ||
| TLR9 | 0 | Protective role against alveolar bone loss in the absence of Porphyromonas gingivalis | ||
| IL18 | 15 | Inflammation and modulation of the activity of macrophages and neutrophils. Significantly higher in patients with chronic periodontitis compared to healthy controls |
||
| IFNB1 | 0 | TNFa, via the autocrine action of IFNbeta, differentially regulates the expression of proinflammatory genes and DNA synthesis | ||
| GLT6D1 | 2 | rs1537415 | Genome-wide significant association with aggressive periodontitis | Schaefer et al. [12] |
| IL1B | 8 | The carriage rate of the R allele (frequency of N/R and R/R genotypes) among cases and controls | Laine et al. [13] | |
| IL1RN | 13 | |||
| IL6 | 14 | |||
| IL10 | 7 | |||
| VDR | 23 | |||
| CD14 | 29 | |||
| TLR4 | 4 | |||
| MMP1 | 11 |
aGene names in bold were not used in the analysis because they were not well represented on the Infinium HumanMethylation450k array
bNumber of probes annotated to map to each gene in Infinium HumanMethylation450k array