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 Table of Contents  
Year : 2014  |  Volume : 2  |  Issue : 1  |  Page : 3-7

Single nucleotide polymorphisms and periodontitis

1 Department of Oral Pathology and Microbiology; Department of Orthodontics, Faculty of Dentistry, Sebha University, Sebha Sebha University, Sebha, Libya
2 Department of Orthodontics, Faculty of Dentistry; Department of Periodontology and Implantology, Sebha University, Sebha Sebha University, Sebha, Libya
3 Department of Microbiology, Faculty of Medicine, Sebha University, Sebha, Libya
4 Department of Orthodontics, Faculty of Dentistry, Sebha University, Sebha, Libya
5 Department of Oral and maxillofacial surgery, Sebha University, Sebha, Libya
6 Department of Periodontics, Faculty of Dentistry, Benghazi University, Benghazi, Libya

Date of Web Publication28-Apr-2014

Correspondence Address:
Ramalingam Karthikeyan
Department of Oral Pathology and Microbiology, Faculty of Dentistry, Sebha University, Sebha
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/2348-1471.131556

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The susceptibility to various diseases is studied with association to genetic polymorphisms. Among these polymorphisms, single-nucleotide polymorphisms (SNPs) are very common throughout the genome. The recent advances in genetic assay techniques and increase in SNP databases are paving a way for investigation of susceptibility genes for periodontitis. This article attempts to review the role of SNP and its implications in periodontal disease and management.

Keywords: Aggressive, chronic, periodontitis, single-nucleotide polymorphisms

How to cite this article:
Karthikeyan R, Peeran SW, Murugan M, Awidat K, Basheer O, Al Mugrabi MH. Single nucleotide polymorphisms and periodontitis. Dent Med Res 2014;2:3-7

How to cite this URL:
Karthikeyan R, Peeran SW, Murugan M, Awidat K, Basheer O, Al Mugrabi MH. Single nucleotide polymorphisms and periodontitis. Dent Med Res [serial online] 2014 [cited 2023 Mar 31];2:3-7. Available from: https://www.dmrjournal.org/text.asp?2014/2/1/3/131556

  Introduction Top

Periodontitis, an oral inflammatory disease with destruction of periodontal tissues, is a complex disease associated with multiple genetic factors and oral environmental factors. [1] Periodontal disease is regarded as a multifactorial condition that occurs because of interplay between environmental, behavioral, microbial and genetic factors. Genetic studies have revealed the polygenic nature of chronic periodontitis. [2]

SNPs are DNA sequence variations that result from the alteration of a single nucleotide, and some SNPs are population-specific. SNPs in these genes do not result in amino-acid substitution but can alter gene function and/or alter gene expression. [1] More than 10 million single-nucleotide polymorphisms (SNPs) have been identified in the human genome. [3]

A single genetic variation may play only a moderate or limited role in common diseases, but it may have important interactions with other genetic variations or environmental factors. [4] Most of the genetic research in the oral disease has focused on gene polymorphisms that play a role in the immune response, tissue destructive process, or metabolic mechanism. In some situations, genetic polymorphisms could cause a change in the protein or its expression, possibly resulting in alterations in innate and adaptive immunity and may thus be deterministic in disease progression. On the other hand, genetic polymorphisms may also act like a protector or a destructive factor for a disease. [5] It is thought that SNP analysis will facilitate in identifying multiple genes associated with periodontitis as genetic markers. By acting as genomic markers, SNPs can aid in clarifying risk factors for complex diseases. [1]

Ten to twenty genes may be involved in such complicated multifactorial disease. [2] Recent reports have indicated that allelic variation in cytokine genes and factors regulating their expression may influence the clinical outcome, susceptibility and progression of periodontal disease. Dysregulation of cytokine gene expression may be responsible for the repeated cycles of tissue inflammation observed in these disorders. [6]

Thus, not only gene-gene interactions but also gene-environment interactions form a complex network in which the disease can initiate and progress. Using decision tree analysis, the presence of bacterial species Tannerella forsythia, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and SNPs TNF-857 and interleukin (IL)-1A -889 were identified as discriminators between periodontitis and non-periodontitis. [7]

Some previous studies have shown associations between periodontitis and SNPs in the IL1, IL10, TNF-α and Fc-γ genes. The SNPs in TRAF1 gene was associated with aggressive periodontitis (AgP) and MMP9 gene was associated with chronic periodontitis (CP). Suzuki et al. investigated the associations between 637 SNPs in 244 genes related to systemic diseases and severe periodontitis on a large scale. They reported that SNPs in the GNRH1, PIK3R1, DPP4, FGL2 and CALCR genes are genomic markers for severe periodontitis. [7] Association between periodontitis and specific genotypes such as PECAM-1, MMP-1, BMP-4, human leukocyte antigen (HLA), vitamin D receptors (VDR), N-formyl peptide receptors, vascular endothelial growth factor (VEGF), transforming growth factor (TGF), Alpha-1-antichymotripsin, hydroxy-methyl-glutaryl CoA reductase, interferon-α, resistin-420, β-defensin, C-reactive protein (CRP), calcitonin receptor gene polymorphisms. [3],[8],[9],[10],[11],[12],[13] Several localized AgP loci on chromosomes 1, 4, 6 and 9 have been identified by parametric linkage analysis. [9]

Racial variations

Generally, the allele frequencies of SNPs differ greatly among races. The IL-1β 13953 SNP that was suggested to be associated with the severity of periodontitis in Caucasians and Mongolian population were extremely low in Chinese populations and rarely detected in Japanese periodontitis patients or in healthy subjects. Tumor necrosis factor (TNF)-α -1031/-863 and -857 SNPs are associated with severe adult periodontitis in Japanese populations. [14]

Rare G allele of rs689466 among Chinese patients andrs20417 among Taiwanese population was associated with CP. [15] Disease association of COX-2 rs6681231 in a population of Northwestern European ethnicity, rs 20417 [15] and COX-2-765 polymorphism to be associated with AgP in Taiwanese. [16]

Interleukin, IL-1β13954 was reported to be associated with risks of AgP in Caucasians and Chileans, but was not associated with AgP in Hispanic, Chinese, Greek and Japanese individuals. Based on the literature, AgP was associated with polymorphisms of IL-1B13954, TLR4 (299), FcγRIIa-H131 and NADPH genes in Caucasians; IL-6R, FcαRI324, IL6ST, PTGDS, COL4A1, COL1A1, KRT23 and IL-1RN (VNTR) genes in Japanese; and MMP-1-1607, IL-1A14845, IL-1B-511 and ER-a in Chinese. [16]

Rate of IL-1a (+4845), IL-1b (+3954), and IL-1RN (VNTR) tended to be lower in Japanese than Caucasians, whereas the rate in African-Americans was between the Caucasian and the Japanese data. [6] The IL1 positive genotype has been reported in 30% Caucasian North Europe, 43% Spanish, 35.3% Swiss Caucasian, 38.9% Australian Caucasian, 34.8% New Zealand, 26% Mexican, 44.4% Greek, 34.4% Polish and 1.6% Chinese samples. SNPs at - 889 of IL1A and + 3953 of IL1B was noted in Caucasian-Portuguese population. [5] The - 44 CC genotype of the β-defensin-1 gene (DEFB1 rs1800972) may be associated with susceptibility to chronic periodontitis in Japanese. [10]

Interleukins and TNF

Genetic polymorphism in cytokine genes is regarded as a promising factor in inducing periodontal diseases. [2] The genes for IL-1α, IL-1β and IL-(1RNa) are all located on the long-arm of chromosome 2. [6] The SNPs in the IL10 gene at positions -1087, -819 and -592 from the transcriptional start site, which have been associated with altered synthesis of IL10 in response to inflammatory stimuli. [17]

Increased prevalence of the GG genotype was observed for the IL-6-174 polymorphism and may be more prone to developing periodontitis. [18] Genes that encode IL-6Ra were located on chromosomes 1q21 and 9, although the gene on chromosome 9 was found out to be a pseudo gene. IL6R 148892 A/C polymorphism could act as a risk factor for periodontitis. [19]

Some TNF-α and IL-1β SNPs, TNF-α -308, -238, -1031, -863 and -857, variants of which are observed in a relatively large proportion of Japanese, have been identified, and the variant alleles of these SNPs have been suggested to be related to high TNF-α production. TNF-α -308 SNP have been associated with an eight-fold higher transcriptional activation rate in vitro.[14]

IL-1β 13953, -511, -31 have been identified. IL-1β 13953 SNP is the one most studied with respect to severity of periodontitis and was associated with a four-fold increase in IL-1β production. Therefore, these SNPs could be candidate SNPs associated with the severity of periodontitis. [14] Allele 2 of IL1A and IL1B are associated with severe peri-implantitis and determined the success of dental implants. [5]

IL-8 -251 (A/T) single nucleotide polymorphism affects the function of promoter gene and cases presenting with AA genotype produce and release higher levels of IL-8 compared to individuals with AT or TT genotype but could not correlate with severity of periodontitis. The IL-8 -4073 gene promoter was associated with CP in non-smoker Brazilian subjects and the frequency of the A allele was higher in the disease group. [2]

IL12RB2 SNPs influence the responses of cell-mediated immunity to periodontal pathogens and contribute to periodontal disease susceptibility. [20]

TNFα haplotype combination (c.-308G > A and c.-238G > A) could not be proven to be an independent risk factor in periodontitis in general and CP or in AgP. Accordingly, no influence of TNFα promoter polymorphisms (c.-1031T > C, c.-863C > A, c.-857C > T) on the occurrence of periodontitis was detected in several studies. [21] Genetic background of TNFα could be regarded as a modulator of clinical features of periodontitis in coronary patients. [22]


The human COX-2 gene, mapped to chromosome 1q25.2-q25.3. In periodontitis, specific COX-2 expression has been reported in gingival tissues. The SNPs within the COX-2gene have been related to increased susceptibility to inflammatory diseases. Genetic linkage analysis performed at localized AgP (LAP) families showed that LAP was linked to chromosome 1q25, covering the COX-2 gene and it is likely that the − 765C allele is protective for periodontitis. [16]


Complement component deficiencies and increased cleavage seem to be associated with severe CP. The C5 polymorphisms is associated with increased severity of inflammation and periodontal destruction. The C5 gene is located on chromosome 9q34.1. The SNP rs17611 of the C5 gene was more prevalent in the periodontitis patient group than in periodontitis-free controls and, together with smoking, may be associated with periodontitis among the Hong Kong Chinese population. [23]


FcγRs are cell-surface receptors for the constant (Fc) region of IgG antibodies. Three different classes of human FcγR family are currently recognized and they encompass 8 genes namely, CD64, encoded by FcγRIa, Ib and Ic genes; CD32, encoded by FcγRIIa, IIb, and IIc genes; CD16, encoded by FcγRIIIa and IIIb genes. [4] Van der Pol et al., reported that FcγRIIA, FcγRIIB, FcγRIIIA and FcγRIIIB are mapped within 3.5cR on chromosome 1, band q23-24. The FcγRIIB-nt645 + 25A/G could be a susceptibility SNP for periodontitis. The FcγRIIBI232T in patients with periodontitis was associated with an increase in the serum-specific IgG2 level against the outer membrane protein from P. gingivalis. [24] Genetic variations of Fragment Crystallizable Gamma Receptor (FcGR), may modify the transcription and hence expression and biological functions of the corresponding receptor molecule, thereby modifying humoral immune responses and influencing one's susceptibility to periodontitis. [4]


Platelet endothelial cell adhesion molecule-1 (PECAM-1/CD31) is encoded by a 75 kb gene that resides at the end of the long arm of chromosome 17. The Arg670Gly polymorphism in this exon has been found to be related to diseases such as ischemic heart diseases, myocardial infarction (MI) and stenosis but no significant association with periodontal disease. [25]


The S100A8 protein belongs to the family of calcium-binding S100 proteins. The S100A8 gene is a member of the S100 gene cluster on chromosome1q21. The genes S100A8, S100A9 and S100A12 form a secondary cluster, which is adjacent to the core cluster. It encodes a structural protein of 93 amino acids called S100A8. Many studies have demonstrated that the concentration of S100A8 and/or calprotectin in gingival crevicular fluid correlated with both gingivitis and periodontitis. The SNP rs3795391 does not affect the structure of gene products, but it might cause quantitative differences in gene expression and might affect the susceptibility of AgP. [9]


Toll-like receptors (TLRs) are key sensors of the innate immune system. The TLR2 gene products were found to be upregulated in inflamed gingival tissue. Genetic association studies on TLR2 hitherto did not identify an association of SNPs with AgP or CP. Case-control association study of eight tag SNP, which spanned 23 kb of the complete coding region of TLR2, as well as the resequencing of exon 3 in 47 AgP cases, was not able to identify statistically significant associations of genetic variants of TLR2 with periodontitis [26] Polymorphisms in genes such as TLR4 and CD14 have been associated with increased risk of Gram-negative infections and increase susceptibility to periodontitis. Asp299Gly TLR4 gene polymorphic form is associated with a decreased risk of AgP but not CP in West European Caucasians. [27]


Bone resorption by osteoclasts is one of the main symptoms of periodontal and peri-implant diseases. Osteoclastogenesis is controlled by three members of the TNF and TNF-receptor super family: Receptor activator of nuclear factor-kappa B ligand (RANKL), receptor activator of nuclear factor kappa B (RANK) and osteoprotegerin (OPG). The OPG gene is located on chromosome 8q, and is a single-copy gene with five exons. The OPG 950C/T and 1181G/C polymorphisms have been implicated with peri-implantitis but no significant association with chronic periodontitis [8] The RANK/RANKL/OPG regulatory axis is also involved in inflammatory bone destruction induced by pro-inflammatory cytokines such as prostaglandin E2 (PGE2), IL-1b, IL-6, IL-11 and TNF-α. RANK polymorphisms have a minor effect in pathogenesis of AgP. [28]

  Genome Wide Association Studies Top

Demmer et al., analyzed the whole genome to show the differential gene expression of healthy and diseased periodontal sites. They identified numerous up- or downregulated genes in disease compared to health, including apoptosis, angiogenesis, response to microbes, antigen presentation, regulation of metabolism and signal transduction. [29]

Divaris et al., on their Genome Wide Association Study (GWAS) identified 6 loci associated to CP. The loci of NPY, NCR2 and EMR1 had concordant effect direction in a replication sample. The locus of NUAK1 was associated with smoking and CP, but not seen in healthy controls. There was a lack of overlap of risk loci for the moderate and severe CP. The precision and validity of the genetic SNP estimates will improve with time when higher density imputations, whole genome sequencing and larger GWAS samples are incorporated into the study. [30]

Li et al., did not find any meaningful association between smoking status and ethnicity with CP. They concluded that individuals carrying MMP1-1607 2G allele were associated with overexpression of MMP-1, consequently contributing to more susceptibility to CP. Their meta-analysis suggested that MMP-1 g.-1607dupG contribute to the elevated risk of CP. [31]

Schaefer et al., demonstrated statistically significant associations of rs2891168, rs1333042, rs1333048 and rs496892 in chromosomal region 9p21.3 with localized AgP and even stronger associations with generalized AgP. Ernst et al., have also confirmed this association in their GWAS. The chromosomal locus on 9p21.3, which encodes CDKN2A, CDKN2B and ARF may represent one of the postulated genetic links between coronary heart disease and periodontitis. [32],[33]


SNPs in introns might affect splicing and/or transcription, and missense SNPs in exons might affect function of its product. Such variations can produce a plethora of diseases from variations in morphology to neoplastic transformation. [34],[35],[36]

As evaluation of the function of SNPs, based only on the nucleotide sequence is still very difficult, further functional analysis of these SNPs is needed to elucidate the molecular mechanism of periodontal disease. [28]

Determining the predisposing genetic factors and specific associated inflammatory biomarkers may help the clinician to choose the most reasonable approach to prevent and control the periodontal condition in patients with high susceptibility of periodontal diseases. [2]

Disease biomarkers in saliva are used as a diagnostic tool to screen oral and systemic health. Identification of the qualitative changes in these biomarkers can help in identifying patients with increased susceptibility, sites with active disease, prediction of future-active sites and to monitor therapeutic outcomes. [3]

  Conclusion Top

With advances in technology and growth in genetic knowledge, a world-wide database could be prepared in the near future with a summary of various genomic markers and its clinical implications in various types of periodontitis. It can pave the way for prompt diagnosis, screen susceptible individuals and develop new strategies to modulate their treatment plan.

  References Top

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