KR102543907B1 - A genetic marker for evaluating risk of periodontitis - Google Patents

Abstract

The present invention relates to a single nucleotide polymorphism (SNP) marker for screening for the risk of developing periodontal disease, and more particularly, to a composition containing an agent capable of detecting the marker, a kit containing the composition, and periodontal disease using the marker It relates to a method of providing information for determining the risk of an outbreak.

Description

Genetic marker for evaluating the risk of periodontal disease {A genetic marker for evaluating risk of periodontitis}

It relates to a SNP marker for periodontal disease risk screening, a composition for periodontal disease risk screening including an agent capable of detecting the marker, and a kit containing the composition. In addition, it relates to a method of providing information for determining the risk of developing periodontal disease using the marker.

Periodontal disease is a chronic inflammatory disease, which is caused by bacterial infection of supporting tissues around teeth. Pathological destruction of alveolar bone by periodontal disease is an irreversible progression, and periodontal disease is a major cause of tooth loss in adults. Severe periodontal disease, which can lead to tooth loss, affects 5-20% of the adult population worldwide. The incidence of periodontal disease in Korea is reported to be 10.2 to 55.7% depending on age.

These periodontal diseases are known as two major oral diseases together with dental caries. As causes of periodontal disease, reduction in immunity due to smoking, stress, diabetes, blood diseases, and the like, oral bacteria, and the like are known. In particular, periodontal disease progresses chronically without pain in the early stages, making early detection difficult.

On the other hand, twin studies suggest that genetic factors play an important role in the development of chronic periodontal disease. In addition, to date, various candidate genes and single nucleotide polymorphisms (SNPs) associated with periodontal disease have been suggested.

In previous GWAS studies, genes such as NIN, EMR1, KCNK1, UHRF2, and FBXO38 were reported to be involved in periodontal disease (Divaris et al. 2012, 2013, Rhodin et al. 2014), and TENM2 (teneurin transmembrane protein 2) Although it has been reported to be a candidate gene associated with periodontal disease, the present inventors have identified for the first time that a SNP present on low-density lipoprotein receptor class A domain-containing protein 4 (LDLRAD4) is associated with periodontal disease.

Accordingly, the present inventors have completed the present invention, focusing on the fact that periodontal disease can be prevented or diagnosed early and treated by determining the risk of periodontal disease using the SNP marker.

One object of the present invention is a periodontal treatment comprising at least one single nucleotide polymorphism (SNP) marker selected from the group consisting of the 100th base of SEQ ID NO: 1, the 101st base of SEQ ID NO: 2, and the 101st base of SEQ ID NO: 3 It is to provide SNP markers for disease risk screening.

Another object of the present invention is to include a probe capable of detecting a polynucleotide composed of any one of the nucleotide sequences of SEQ ID NOs: 1 to 3, or a polynucleotide complementary thereto, or a primer capable of specifically amplifying it , To provide a composition for screening the risk of developing periodontal disease.

Another object of the present invention is to provide a kit for determining the risk of developing periodontal disease comprising the composition.

Another object of the present invention is to (a) amplify or probe the nucleotide sequence of a polymorphic site of a polynucleotide consisting of any one of the nucleotide sequences of SEQ ID NOs: 1 to 3 from DNA of an isolated sample, or a polynucleotide complementary thereto It is to provide an information providing method for determining the risk of developing periodontal disease, comprising hybridizing with and (b) determining the base of the polymorphic site amplified or hybridized in step (a).

In order to achieve the above object, one aspect of the present invention is one or more single nucleotide polymorphisms (SNPs) selected from the group consisting of the 100th base of SEQ ID NO: 1, the 101st base of SEQ ID NO: 2, and the 101st base of SEQ ID NO: 3 SNP markers for periodontal disease risk screening including markers are provided.

SEQ ID NOs: 1 to 3 are polymorphic sequences including polymorphic sites. A polymorphic sequence means a sequence containing a polymorphic site including a SNP in a polynucleotide sequence. The polynucleotide sequence may be DNA or RNA.

SEQ ID NO: 1 shows a part of the sequence of chromosome 5, and includes the SNP for screening the risk of developing periodontal disease of the present invention at base 166,677,319 of the entire sequence of chromosome 5, and SEQ ID NOS 2 to 3 are chromosome 18 SNPs for periodontal disease risk screening of the present invention are included at bases 13,181,184 and bases 13,180,107 of the entire sequence of chromosome 18, respectively.

As used herein, the term “polymorphism” refers to the case in which two or more alleles exist in one locus, and among polymorphic sites, only a single base differs from person to person. These are called polymorphisms (SNPs). Preferred polymorphic markers have two or more alleles that exhibit a frequency of greater than 1%, more preferably greater than 5% or greater than 10% in a selected population.

As used herein, the term "allele" refers to several types of a gene present in the same locus of a homologous chromosome. Alleles are also used to indicate polymorphism, for example, SNPs have two types of alleles.

Specifically, the 100th base of SEQ ID NO: 1 may be A or C, the 101st base of SEQ ID NO: 2 may be G or A, or the 101st base of SEQ ID NO: 3 may be G or A.

More specifically, when the 100th base of SEQ ID NO: 1 is C, it can be determined that the risk of developing periodontal disease is low, the 101st base of SEQ ID NO: 2 is A, or the 101st base of SEQ ID NO: 3 If is A, it can be determined that the risk of developing periodontal disease is high.

In addition, the SNP marker of the 100th base of SEQ ID NO: 1 is described as rs424220, the SNP marker of the 101st base of SEQ ID NO: 2 is described as rs12969041, and the SNP marker of the 101st base of SEQ ID NO: 3 is rs2027756 may be described.

The term "rs_id" of the present invention refers to an rs-ID, an independent marker assigned to all SNPs registered by NCBI. In the present invention, it is described in the form of rs4242220. Such rs_id means a SNP marker, which is a polymorphic marker of the present invention. A person skilled in the art can easily identify the location and sequence of the SNP using the rs_id. The specific sequence corresponding to NCBI's dbSNP number, rs_id, may change slightly over time. It will be apparent to those skilled in the art that the scope of the present invention also extends to the altered sequence.

In addition, the sequence of SEQ ID NO: 1 may be located on teneurin transmembrane protein 2 (TENM2) gene, and the SNP marker of SEQ ID NO: 2 and the SNP marker of SEQ ID NO: 3 are LDLRAD4 (low-density lipoprotein receptor class A domain- containing protein 4) may be located on a gene.

The term of the present invention, “teneurin transmembrane protein 2 (TENM2)” is known to be involved in ApoE gene expression, thereby affecting lipid metabolism in the blood, as well as being involved in the development and formation of the nervous system and signal transduction in cells.

The term of the present invention, “LDLRAD4 (low-density lipoprotein receptor class A domain-containing protein 4)” is involved in the influx of cholesterol into cells, is involved in the regulation of blood lipid concentration, and also functions as a TGF-beta signal transduction regulator. , It is known to be involved in cell proliferation, differentiation, apoptosis, and immunosuppression.

The SNP markers of the present invention are the markers shown in Table 2, and can be determined as individuals having a high risk of periodontal disease or having a high risk of periodontal disease.

The term of the present invention, "periodontal disease" refers to periodontal disease caused by various causes, and as risk factors, overall health conditions such as periodontal microbes, smoking, cardiovascular disease, and metabolic syndrome are known. In addition, age, gender, socioeconomic status and lifestyle can also cause periodontal disease. The SNP marker provided in the present invention can determine whether or not there is a risk of developing periodontal disease.

In one embodiment of the present invention, as a result of analyzing genotypes associated with periodontal disease through GWAS research, it was confirmed that the SNP markers of the present invention are associated with the risk of developing periodontal disease (Example 2, Table 2).

In another aspect, the present invention provides a composition for periodontal disease risk screening, comprising a probe capable of detecting a marker for determining the risk of developing periodontal disease, or an agent capable of specifically amplifying it.

The term of the present invention, "probe capable of detecting the risk of developing periodontal disease" means a composition capable of determining the risk of developing periodontal disease by specifically hybridizing with the polymorphic region of the gene as described above, , The specific method of such genetic analysis is not particularly limited, and may be by any gene detection method known in the art to which this invention belongs.

The term of the present invention, "an agent capable of amplifying a marker for detecting the risk of developing periodontal disease" means a composition capable of determining the risk of developing periodontal disease by confirming the polymorphic region of the gene as described above through amplification, preferably More specifically, it means a primer capable of specifically amplifying the polynucleotide of the marker.

Primers used for amplification of the polymorphic marker refer to single-stranded oligonucleotides that can act as starting points for template-directed DNA synthesis under appropriate conditions and appropriate temperatures in an appropriate buffer. The appropriate length of the primer may vary depending on the purpose of use, but is usually 15 to 30 nucleotides. Short primer molecules generally require lower temperatures to form stable hybrids with the template. The primer sequence need not be completely complementary to the template, but must be sufficiently complementary to hybridize with the template.

In the present invention, the term "primer" is a base sequence having a short free 3' terminal hydroxyl group, which can form a base pair with a complementary template and is the starting point for copying the template strand. A short sequence that functions as a point. A primer can initiate DNA synthesis in the presence of a reagent for polymerization (i.e., DNA polymerase or reverse transcriptase) and four different nucleoside triphosphates in an appropriate buffer and temperature. The risk of developing periodontal disease can be predicted through PCR amplification to determine whether a desired product is produced. PCR conditions and lengths of sense and antisense primers can be modified based on those known in the art.

The probes or primers of the present invention can be chemically synthesized using the phosphoramidite solid support method, or other well-known methods. Such nucleic acid sequences can also be modified using a number of means known in the art. Non-limiting examples of such modifications include methylation, "capping", substitution of one or more homologues of a natural nucleotide, and modifications between nucleotides, such as uncharged linkages such as methyl phosphonates, phosphotriesters, phosphoroamidates, carbamates, etc.) or to charged linkages (eg phosphorothioates, phosphorodithioates, etc.).

In another aspect, the present invention provides a kit for screening the risk of developing periodontal disease comprising the composition for screening the risk of developing periodontal disease.

The kit may be a RT-PCR kit or a kit for DNA analysis (eg, a DNA chip).

The kit of the present invention can check the risk of periodontal disease by confirming the SNP marker for screening the risk of periodontal disease through amplification or by checking the expression level of the SNP marker to the mRNA expression level. As a specific example, the kit for measuring the mRNA expression level of a marker for screening for the risk of developing periodontal disease in the present invention may be a kit including essential elements required to perform RT-PCR. In addition to each primer pair specific for the gene of the marker for periodontal disease risk screening, the RT-PCR kit contains a test tube or other suitable container, a reaction buffer (with varying pH and magnesium concentration), and deoxynucleotide. (dNTPs), enzymes such as Taq-polymerase and reverse transcriptase, DNase, RNAse inhibitors, DEPC-water, sterile water, and the like. It may also include a primer pair specific to a gene used as a quantitative control. Also preferably, the kit of the present invention may be a kit for screening for the risk of developing periodontal disease, including essential elements necessary for performing DNA chip. A DNA chip kit is a DNA chip kit in which nucleic acid species are attached in a gridded array to a generally flat solid support plate, typically a glass surface no larger than a slide for a microscope, and nucleic acids are regularly arranged on the chip surface. It is a tool that enables mass parallel analysis by multiple hybridization reactions between nucleic acids on the chip surface and complementary nucleic acids included in the solution treated on the chip surface.

In another aspect, the present invention provides (a) a polynucleotide consisting of any of the nucleotide sequences of SEQ ID NOs: 1 to 3 from the DNA of the separated sample, or amplifying or probe the nucleotide sequence of the polymorphic site of the polynucleotide complementary thereto hybridizing with; and (b) determining the base of the amplified or hybridized polymorphic site in step (a), providing information for determining the risk of developing periodontal disease.

The DNA of the isolated sample may be obtained from a sample isolated from an individual.

As used herein, the term "subject" refers to a subject for determining the risk of developing periodontal disease, and DNA is obtained from samples such as hair, urine, blood, various body fluids, separated tissues, isolated cells, or saliva from the specimen. It can be done, but is not limited thereto.

Any method known to those skilled in the art may be used for amplifying the polymorphic site of the SNP marker from DNA in step (a) or hybridizing with a probe. For example, it can be obtained by amplifying a target nucleic acid through PCR and purifying it. Other ligase chain reaction (LCR) (Wu and Wallace, Genomics 4, 560 (1989), Landegren et al., Science 241, 1077 (1988)), transcription amplification (Kwoh et al., Proc. Natl. Acad. Sci. USA 86, 1173 (1989)) and self-maintained sequence cloning (Guatelli et al., Proc. Natl. Acad. Sci. USA 87, 1874 (1990)) and nucleic acid-based sequence amplification (NASBA) can be used.

Determining the base of the polymorphic site in step (b) is sequence analysis, hybridization by microarray, allele specific PCR (allele specific PCR), dynamic allele-specific hybridization (DASH) , PCR extension analysis, PCR-SSCP, PCR-RFLP analysis or TaqMan techniques, SNPlex platform (Applied Biosystems), mass spectrometry (eg, MassARRAY system from Sequenom), mini-sequencing methods, Bio-Plex systems (BioRad), CEQ and SNPstream systems (Beckman), Molecular Inversion Probe array technologies (eg, Affymetrix GeneChip), and BeadArray Technologies (eg, Illumina GoldenGate and Infinium assays). By these methods or other methods available to those skilled in the art, one or more alleles in a polymorphic marker, including microsatellites, SNPs or other types of polymorphic markers, can be identified. Determination of the base of such a polymorphic site can be preferably performed through an SNP chip.

As used herein, the term "SNP chip" refers to one of DNA microarrays capable of identifying each base of hundreds of thousands of SNPs at once.

The TaqMan method includes (1) designing and constructing primers and TaqMan probes to amplify a desired DNA fragment; (2) labeling probes of different alleles with FAM dye and VIC dye (Applied Biosystems); (3) performing PCR using the DNA as a template and using the primers and probes; (4) after the PCR reaction is completed, analyzing and confirming the TaqMan assay plate with a nucleic acid analyzer; and (5) determining the genotypes of the polynucleotides of step (1) from the analysis results.

In the above, sequencing analysis may use a conventional method for nucleotide sequence determination, and may be performed using an automated genetic analyzer. In addition, allele-specific PCR refers to a PCR method of amplifying a DNA fragment where the SNP is located with a primer set including a primer designed with the base where the SNP is located as the 3' end. The principle of the method is, for example, when a specific base is substituted from A to G, a primer containing the A as the 3' terminal base and a primer in the opposite direction capable of amplifying a DNA fragment of an appropriate size are designed to perform PCR. When performing the reaction, when the base at the SNP position is A, the amplification reaction is normally performed and a band at the desired position is observed. When the base is substituted with G, the primer can complementarily bind to the template DNA, but 3 ' This is because the amplification reaction is not performed properly because the terminal side does not make complementary bonds. DASH can be performed by a conventional method, preferably by a method by Prince et al.

On the other hand, PCR extension analysis first amplifies a DNA fragment containing the base where the single nucleotide polymorphism is located with a primer pair, and then inactivates it by dephosphorylating all nucleotides added to the reaction, whereby a SNP-specific extension primer, A primer extension reaction is performed by adding a dNTP mixture, dideoxynucleotide, reaction buffer and DNA polymerase. At this time, the extension primer takes the base immediately adjacent to the 5' direction of the base where the SNP is located as the 3' end, and the dNTP mixture excludes nucleic acids having the same base as the dideoxynucleotide, and the dideoxynucleotide represents the SNP. It is selected from one of the base types. For example, when there is a substitution from A to G, when a mixture of dGTP, dCTP and TTP and ddATP are added to the reaction, the primer at the base where the substitution occurs is extended by DNA polymerase, and after a few bases, A The primer extension reaction is terminated by ddATP at the position where the base first appears. If the substitution does not occur, since the extension reaction is terminated at that position, the base type representing the SNP can be determined by comparing the lengths of the extended primers.

At this time, as a detection method, when the extension primer or dideoxynucleotide is fluorescently labeled, the SNP can be detected by detecting fluorescence using a genetic analyzer (eg, ABI Model 3700, etc.) used for general base sequence determination. In the case of using unlabeled extended primer and dideoxynucleotide, the SNP can be detected by measuring molecular weight using matrix assisted laser desorption ionization-time of flight (MALDI-TOF) technique.

Specifically, among the nucleotide sequences determined in step (b), when the 100th base of SEQ ID NO: 1 is C, it can be determined that the risk of developing periodontal disease is low, and the 101st base of SEQ ID NO: 2 is A, Alternatively, when the 101st base of SEQ ID NO: 3 is A, it can be determined that the incidence of periodontal disease is high.

The present invention determines the risk of periodontal disease using SNP markers located on TENM2 (teneurin transmembrane protein 2) or LDLRAD4 (low-density lipoprotein receptor class A domain-containing protein 4) to treat periodontal disease that is difficult to detect early. disease can be predicted and treated.

1 is a diagram showing a Manhattan plot of a genomewide association study (GWAS) for chronic periodontal disease cases and controls. (a) shows the results of moderate and severe cases, (b) the results of moderate cases and (c) the results of severe cases. Single nucleotide polymorphisms (SNPs) are represented based on physical chromosomal location (horizontal axis) along with -log ₁₀ (p-value) (vertical axis). The blue line represents the association threshold for moderate or severe periodontal disease at the p-value = 5 × 10 ^-5 level (a) or at the p-value = 1 × 10 ^-5 level (b and c). Genes indicated by red dots indicate MAF > 2.0, and genes indicated by red circles indicate genes verified by the two-step analysis.

Hereinafter, the present invention will be described in more detail through examples. These examples are only for illustrating the present invention, and the scope of the present invention is not construed as being limited by these examples.

Example 1. Design and preparation of experiments for the selection of periodontal disease-related markers

1-1. Experimental Design and Ethical Considerations

The present invention was based on the results of genomewide association study (GWAS) for periodontal disease. Specifically, samples and data from the Korea Centers for Disease Control and Prevention's Korea Genome Analysis Project (4845-301), Korean Genome Epidemiology Investigation Project (4851-302), and Korean Human Resources Bank Project (4851-307, KBP-2014-15) were utilized. Thus, the periodontal disease-related markers of the present invention were discovered. The outcome variable is periodontal disease, and the main variable to explain this is the SNP.

The present invention was approved by the Institutional Inspection Committee for Human Subjects at Seoul National University Dental Hospital (approval number: ERI14001), and all participants voluntarily participated in this study and gave written consent.

1-2. study object

Participants were selected from the ongoing Korean Genome and Epidemiologic Study (KoGES) cohort. Participants were recruited from a cohort in Yangpyeong-si, Korea.

Initially, a total of 3,262 residents were enrolled in the KoGES from 2004 to 2008 as part of the health cohort in Yangpyeong. Among them, 2,117 residents were tracked, and they underwent health and dental examinations from 2010 to 2013, the third phase of KoGES. When selecting participants for DNA analysis, priority was given to healthy residents without significant systemic disease. Only 732 residents were registered with the Korea GWAS Bank to conduct DNA genetic research.

The 732 participants selected from the original cohort were adults without self-reported metabolic disease (type 2 diabetes, hypertension or hyperlipidemia), cardiovascular disease (myocardial infarction, stroke) or cancer. Their blood pressure ranges (SBP<130 mmHg and DBP<90 mmHg) and fasting blood glucose (<126 mg/dl) were normal during the health examination period.

Finally, the final cohort for GWAS analysis consisting of 677 participants was selected by applying the following exclusion criteria. i) Participants with missing factor, ii) Residual natural teeth <2.

The final cohort was identical to the first cohort in terms of age, gender, smoking, alcohol consumption, and body mass index, but differed in educational level.

1-3. population characteristics

Among the 677 participants selected above, there were 60 people without periodontal disease, 203 people with mild periodontal disease, 314 people with moderate periodontal disease, and 314 people with severe periodontal disease. There were 100 patients with periodontal disease. The control group (no periodontal disease or mild periodontal disease) consisted of 263 patients, moderate periodontal disease patients 314 patients, and severe periodontal disease patients 100 patients (Table 1). Compared to the control group, the proportion of men, smokers and drinkers was higher in patients with moderate periodontal disease and patients with severe periodontal disease.

In Table 1 below, BMI represents body mass index (kg/m ² ), and the bolded values show statistical significance at p-value<0.05, and the values are T-test ^* , Chi-square test ^† , and ANOVA ^‡ saved by ^§ Control means normal or mild periodontal disease, ^¶ Case means chronic periodontal disease judged by CDC/AAP criteria.

1-4. Periodontitis assessment

The history of periodontal disease was evaluated by panoramic radiograph obtained by digital panoramic X-ray (Pax-Primo, Vatech Global, Seoul, Korea).

Radiographic alveolar bone loss (RABL), which is the distance from the cement enamel junction (CEJ) to the alveolar bone ridge, is measured by a skilled dentist on the mesial and distal sides of all teeth. It was obtained by measuring in units of 0.1 mm. All measurements were automatically adjusted to fit the magnification factor by an image viewer program.

When an unclear CEJ was found due to prosthetic devices or overlapping teeth, an arbitrary CEJ was applied with reference to the CEJ of adjacent teeth. In the case of vertical bone defects or differences in the oral and lingual bones, a low value of bone destruction was applied. Regarding test-retest reliability, according to a cutoff value of 6 mm, RABL showed a kappa value of 0.69. Compared to the gold standard for alveolar bone loss measured during periodontal valve surgery, the sensitivity and specificity of RABL were 0.62 and 0.79, respectively (Korea Centers for Disease Control and Prevention).

Based on CDC/AAP criteria, we classified participants into four categories; Normal, mild periodontal disease (interdental area of 2 or more 3 mm ≤ RABL ≤ 4 mm), moderate periodontal disease (interdental area of 2 or more 4 mm ≤ RABL ≤ 6 mm (not the same tooth)), and moderate periodontal disease (2 or more) Interdental region of 6 mm ≤ RABL (not the same tooth)) (Eke et al. 2012).

For the GWAS of periodontal disease, the present inventors set normal and mild periodontal disease patients as controls, and moderate periodontal disease patients and severe periodontal disease patients as cases.

1-5. Genotyping and quality assessment

Genotyping of DNA samples isolated from peripheral blood collected from participants in the health cohort in Yangpyeong was performed using Illumina Human1M-duo Beadchip (Illumina Inc., San Diego, CA, USA). 1,010,624 SNPs were analyzed using the Bayesian Robust Linear Modeling (BRLMM) genetic analysis algorithm using the Mahalanobis Distance (Rabbee & Speed 2006). Cases with genotyping accuracy of 98% or less, high missed genotyping call rate (CR) (≥4%), high heterozygosity (≥30%), or gender-specific discrepancies were considered for further study. was excluded from

Pairwise identity-by-state (IBS) was calculated using PLINK (version 1.07) (Purcell et al. 2007), and individuals with a high correlation with an IBS value of 0.8 or higher were excluded. A total of 723,056 SNPs from 677 subjects were analyzed, except for cases with significant deviations from allele frequency (MAF; <0.01) or Hardy-Weinberg equilibrium (p-value <0.01).

Example 2. Selection of SNPs associated with periodontal disease through genomewide association study (GWAS)

As previously known (Divaris et al. 2013), the 723,056 SNPs selected in the above example were combined with three case-control data [moderate and severe cases versus controls (414 versus 263), moderate cases versus controls (314 versus 263) , and severe cases versus controls (100 versus 263)].

Each case-control set was analyzed by multivariable logistic regression, controlling for age, sex, smoking, drinking, education and body mass index as covariates. Statistical analysis was performed using PLINK (version 1.07) (Purcell et al. 2007).

We applied a two-stage analysis to find true-positive relationships (Schaefer et al. 2010): (i) “hypothesis-generating exploratory stage” within the total population including moderate cases, severe cases and controls (ii) ) Validation step using SNPs that pass a pre-selected significant titer in the combined population of moderate cases and controls, and each of the severe case and control populations.

If no significant SNP (p-value < 5 × 10 ^-8 ) is found in the whole genome, p-value < 5 × 10 ^-5 for the total population and p-value < 1 × 10 ^-5 for the subpopulation A suggestive criterion was used. The present inventors also tried to reduce false positives by excluding genes with MAF<0.2.

Sample size for 80% power at α=0.05 was based on YPC parameters including MAF, effect size, and prevalence of chronic periodontal disease in Koreans. The effect size was applied to the odds ratio of each gene (Table 2), and the prevalence of chronic periodontal disease was 10.2 - 55.7% (Kim et al. 2014). Therefore, the sample size of each SNP was calculated ex post.

As a result, at p-value<5×10 ^-8 , no significant SNPs were found in the whole genome, but at p-value<5×10 ^-5 and MAF>0.2, 9 SNPs completed the hypothesis-generating exploration step. passed. The nine SNPs (7 genes) are rs4242220 (TENM2), rs12969041 and rs2027756 (LDLRAD4), rs4704706 (RNUSE-1), rs4783276 (CCDH13), rs10219568 (SLC15A5), rs7257867 (NLRP12), rs6876160 and rs6890619 (RASGRF2) . However, none of the SNPs showed statistical significance at p-value<0.05 after Bonferroni correction.

Furthermore, it was confirmed whether the nine SNPs were independently associated with severe chronic periodontal disease and moderate chronic periodontal disease. In subgroup analysis, we used the criterion of p-value<1×10 ^-5 , and as a result, three SNPs passed the criterion (Table 2).

In Table 2 below, BLK is B lymphoid tyrosine kinase, BP is base pair, Chr is chromosome, L95 is the lower limit of the 95% confidence interval, OR is age, gender, smoking, drinking, education and body mass correction odds ratio, p is the p-value, SNP is the dbSNPrsID, and U95 is the upper limit of the 95% confidence interval. Numerical values in bold mean p-value<1×10 ^-5 , ^† means amino acid change, and ^‡ means allele frequency in the total population (n=677).

Among them, one SNP (rs4242220) was associated with moderate chronic periodontal disease, and two SNPs (rs12969041, rs2027756) were associated with severe chronic periodontal disease. According to FIG. 1 (Manhattan plot), the implicitly associated genes (p-value<1×10 ^-5 ) were TENM2 for moderate cases and LDLRAD4 for severe cases.

Regarding moderate periodontal disease, one SNP (rs424220 on TENM2) was associated with a significantly reduced risk (AOR 0.53, 95% confidence interval (CI): 0.40-0.70, p-value = 8.97 × 10 ^-6 , Table 2).

Regarding severe periodontal disease, two SNPs (rs12969041 and rs2027756 on LDLRAD4) were associated with a significantly increased risk (AOR 2.86, 95% confidence interval (CI): 1.92-4.27, p-value = 2.79 × 10 ^-7 , Table 2). The two SNPs were located in the 5' upstream region of LDLRAD4, and R(r ² ) was 0.963. This suggests that both SNPs are perfectly correlated non-equilibrium and show the same association.

From the above description, those skilled in the art to which the present invention pertains will be able to understand that the present invention may be embodied in other specific forms without changing its technical spirit or essential features. In this regard, the embodiments described above should be understood as illustrative in all respects and not limiting. The scope of the present invention should be construed as including all changes or modifications derived from the meaning and scope of the claims to be described later and equivalent concepts rather than the detailed description above are included in the scope of the present invention.

<110> Seoul National University R&DB Foundation <120> A genetic marker for evaluating risk of periodontitis <130> KPA151035-KR <160> 3 <170> KopatentIn 2.0 <210> 1 <211> 200 <212> DNA <213> Homo sapiens <220> <221> variation <222> (100) <223> N=A or C <400> 1 ctgctggatc tggcctgcag attatttttt atttttatgt catttgccag catttaagaa 60 tcctgagatt taacataaat atttggactt ccagactctn tctttttttt tttaaattcc 120 cgtatttggc aatgtctggc ccacctgcct ggaggtgagt aattgcctgg agctgagtag 180 ttggtgtctc ttttgaatga 200 <210> 2 <211> 201 <212> DNA <213> Homo sapiens <220> <221> variation <222> (101) <223> N=G or A <400> 2 aaatagctca aaaaaataaa tggcctaaaa cagttttcct tgcaagactg cagaagagct 60 gcacaaattg cccttggggag gccaggcgga gggtctctcc ngggatgcat gttcactctt 120 gccacagctg gaggaagcag gccctaaggc ttgcactgca aagtgatgag aatgaagccc 180 tggttatgct agacttcaag g 201 <210> 3 <211> 201 <212> DNA <213> Homo sapiens <220> <221> variation <222> (101) <223> N=G or A <400> 3 agaagctatc aaggaaaaga caggcatttt tttattggt aaaatatgca caacacaaaa 60 tttgcgattt ctaagcatgt ttaagtgtac agttcagtgg nggtaagtac catcacacag 120 ctgtgcaacc atcaccactg gccacccctg taacatttcc gtattctcag cacacaatgt 180 ttgcatactg cacagcaaaa g 201

Claims (12)

delete delete delete delete delete delete delete A composition for screening for the risk of developing periodontal disease, comprising a probe capable of detecting a polynucleotide composed of the nucleotide sequence of SEQ ID NO: 2 or 3, or a polynucleotide complementary thereto, or a primer capable of specifically amplifying it.
A kit for determining the risk of developing periodontal disease comprising the composition of claim 8.
(a) amplifying the nucleotide sequence of the polymorphic site of the polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 2 or 3 or its complementary polynucleotide from the DNA of the separated sample or hybridizing with the probe; and
(b) a method for providing information for determining the risk of developing periodontal disease, comprising the step of determining the base of the polymorphic site amplified or hybridized in step (a).
delete The method of claim 10, wherein of the nucleotide sequence determined in step (b),
When the 101st base of SEQ ID NO: 2 is A; or
If the 101st base of SEQ ID NO: 3 is A, it is determined that the incidence of periodontal disease is high.

Images