Method for determining the risk of developing high risk open angle glaucoma in Koreans specific by polygenic risk score analysis
Patent Information
- Application Number
- KR1020230122405
- Authority / Receiving Office
- KR · KR
- Patent Type
- Patents
- Current Assignee / Owner
- Filing Date
- 2023-09-14
- Publication Date
- 2026-09-18
- Estimated Expiration
- 2043-09-14
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Figure 112023101848988-PAT00001_ABST
Abstract
Description
Technology Field
[0001] The present invention relates to a method for determining the risk of developing high-risk open-angle glaucoma in Koreans by polygenic risk score analysis. Background Technology
[0002] Glaucoma is not caused by daily lifestyle habits, is not contagious, and is not life-threatening; however, along with diabetic retinopathy, it is one of the most common eye diseases causing blindness. In particular, early diagnosis and treatment are crucial because once glaucoma develops, the damaged optic nerve cannot be restored. Although many ophthalmologists are currently conducting research to identify the causes and develop effective treatments, the exact etiology of glaucoma remains unknown.
[0003] Specifically, glaucoma is a degenerative and progressive optic neuropathy characterized by glaucomatous optic nerve damage accompanied by visual field defects. Globally, glaucoma is one of the leading causes of visual field loss and blindness. Recent studies have revealed that open-angle glaucoma (OAG) is phenotypic and genetically heterogeneous and is virtually polygenic.
[0004] Although there have been some studies on the association between glaucoma and gene loci, the specific correlation remains uncertain. Furthermore, predictive methods utilizing polygene risk score analysis based on Genome-wide Association Studies (GWAS) for open-angle glaucoma are currently lacking for East Asian populations, which have a high incidence of glaucoma.
[0005] Accordingly, the inventors investigated the association between the incidence of high-risk glaucoma and loci in a Korean cohort and confirmed that there is a significant association, thereby completing the present invention. Prior art literature
[0006] Republic of Korea Published Patent No. 10-2023-0075213 (May 31, 2023) The problem to be solved
[0007] The objective of the present invention is to provide information necessary for predicting the risk of developing open-angle glaucoma in Koreans by selecting one or more specimens from the group consisting of rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731, and rs9913911 from biological samples. It is to provide a method for identifying single nucleotide polymorphisms (SNPs).
[0008] Another object of the present invention is a biomarker composition for identifying open-angle glaucoma in Koreans comprising one or more single nucleotide polymorphisms (SNPs) selected from the group consisting of rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731, and rs9913911. It is to provide.
[0009] Another objective of the present invention is to provide a composition for predicting the risk of developing open-angle glaucoma, comprising a formulation capable of detecting the biomarker composition.
[0010] Another objective of the present invention is to provide a kit for predicting the risk of developing open-angle glaucoma, comprising the above composition.
[0011] Other objects and advantages of the present invention will become more apparent from the following detailed description of the invention, claims, and drawings. means of solving the problem
[0012] In order to provide information necessary for predicting the risk of developing open-angle glaucoma in Koreans, the present invention provides one or more selected from the group consisting of rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731, and rs9913911 from biological samples. A method for identifying single nucleotide polymorphisms (SNPs) is provided.
[0013] In the present invention, polymorphism refers to the case where two or more alleles exist at a single locus, and among polymorphic regions, a single nucleotide polymorphism (SNP) is defined as a region where only a single nucleotide differs from person to person. A preferred polymorphic marker has two or more alleles that exhibit an occurrence frequency of 1% or more, more preferably 5% or 10% or more, in a selected population. Therefore, genetic association with a polymorphic marker means that there is an association with one or more specific alleles of a specific polymorphic marker. The marker may include alleles of any variant form found in the genome, including single nucleotide polymorphisms (SNPs), microsatellites, insertions, deletions, duplications, and translocations.
[0014] In the present invention, an allele or allelic trait refers to multiple types of a single gene located at the same locus on homologous chromosomes. Alleles are also used to express polymorphism; for example, an SNP has two types of alleles.
[0015] In the present invention, rs_id refers to the rs-ID, an independent marker assigned to all initially registered SNPs by NCBI, which began accumulating SNP information in 1998. In the present invention, it is described in the form of rs2946370. The rs_id listed in such a table refers to the SNP marker, which is a polymorphic marker of the present invention. A person skilled in the art will be able to easily identify the location and sequence of the SNP using the above rs_id.
[0016] rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731, and rs9913911, used in this invention to predict the risk of developing open-angle glaucoma in Koreans, are single nucleotide polymorphism databases of the National Center for Biotechnology Information (NCBI dbSNP, They are each registered at http: / / www.ncbi.nlm.nih.gov / snp / ).
[0017] According to one embodiment of the present invention, in the case of rs2946370C>T, rs66500121G>A, rs4308305C>T, rs9853115A>T, rs28795989G>A, rs61275591G>A, rs2745572G>A, rs1412829G>A, rs2472494C>T, rs11024102C>T, rs4303192C>T, rs35155027C>G, rs150025731A>ACTCACCGG and single nucleotide polymorphisms (SNPs), it can be determined that the risk for open-angle glaucoma is increased, and rs57111852A>G, In the case of single nucleotide polymorphisms (SNPs) such as rs2526101G>A, rs3829849C>T, rs61870251C>A, rs58073046G>A, and rs9913911G>A, it can be determined that the risk of open-angle glaucoma is reduced. In this regard, there were cases where the patient with the highest genetic risk increased the risk of glaucoma by 5.62 times compared to the median.
[0018] In the present invention, the single nucleotide polymorphisms (SNPs) are located in the MIR4778 gene on chromosome 2 in the case of rs2946370, in the CADM2 gene on chromosome 3 in the case of rs66500121, in the FNDC3B gene on chromosome 3 in the case of rs4308305, in the LINC02020 gene on chromosome 3 in the case of rs9853115, in the AFAP1 gene on chromosome 4 in the case of rs28795989, in the C5orf67 gene on chromosome 5 in the case of rs61275591, in the EXOC2 gene on chromosome 6 in the case of rs57111852, in the FOXC1 gene on chromosome 6 in the case of rs2745572, and in the THSD7A gene on chromosome 7 in the case of rs2526101. In the case of rs1412829, it is located in the CDKN2B-AS1 gene on chromosome 9; in the case of rs2472494, it is located in the ABCA1 gene on chromosome 9; in the case of rs3829849, it is located in the LMX1B gene on chromosome 9; in the case of rs61870251, it is located in the LHPP gene on chromosome 10; in the case of rs11024102, it is located in the PLEKHA7 gene on chromosome 11; in the case of rs4303192, it is located in the AGBL2 gene on chromosome 11; in the case of rs58073046, it is located in the ARHGEF12 gene on chromosome 11; in the case of rs35155027, it is located in the SIX1 gene on chromosome 14; in the case of rs150025731, it is located in the LOXL1 gene on chromosome 15; and in the case of rs9913911, it is 17 It may be located in the GAS7 gene on the chromosome.
[0019] In the present invention, the biological sample may be blood, tissue, cell, serum, plasma, saliva, urine, etc., but is not limited thereto.
[0020] In the present invention, the subject of the biological sample may be a Korean.
[0021] In addition, the present invention relates to a biomarker composition for identifying open-angle glaucoma in Koreans comprising one or more single nucleotide polymorphisms (SNPs) selected from the group consisting of rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731, and rs9913911. Provides
[0022] In addition, the present invention provides a composition for predicting the risk of developing open-angle glaucoma, comprising a formulation capable of detecting the biomarker composition.
[0023] In the present invention, the agent capable of detecting the biomarker composition may be a primer or probe that specifically binds to a polynucleotide containing an SNP marker or a polynucleotide complementary thereof, but is not limited thereto.
[0024] In the present invention, the primer or probe that specifically binds to the polynucleotide or its complementary polynucleotide is allele-specific.
[0025] In the present invention, a primer refers to a short nucleic acid sequence having a short free hydroxyl group, capable of forming base pairs with a complementary template, and functioning as a starting point for template strand replication. The primer of the present invention can be chemically synthesized using methods known in the art, such as, for example, the phosphoramidite solid support method.
[0026] In the present invention, the probe refers to a nucleic acid fragment, such as RNA or DNA, composed of several to hundreds of bases that can specifically bind to mRNA, and is labeled so that the presence or absence of a specific mRNA can be confirmed. The probe can be produced in the form of an oligonucleotide probe, a single-stranded DNA probe, a double-stranded DNA probe, an RNA probe, etc., and can be labeled with biotin, FITC, rhodamine, DIG, etc., or labeled with a radioisotope, etc.
[0027] In the present invention, the probe may be labeled with a detectable material, for example, a radioactive label having a suitable signal and a sufficient half-life. The labeled probe may hybridize to nucleic acids on a solid support as known in the literature (Sambook et al., Molecular Cloning, A Laboratory Manual, 1989).
[0028] In the present invention, the probe is an allele-specific probe in which a polymorphic region exists within the nucleic acid fragment, so that it may hybridize to a nucleic acid fragment containing one allele but not to a nucleic acid fragment containing another allele. In this case, the hybridization conditions must be sufficiently strict to ensure that hybridization occurs to only one of the alleles by showing a significant difference in hybridization intensity between the alleles. Preferably, the probe may be single-stranded for maximum efficiency in hybridization, but is not limited thereto.
[0029] In the present invention, the detection of a specific nucleic acid using the primer can be performed by amplifying the sequence of a target gene using an amplification method such as PCR, and then confirming whether the gene has been amplified by a method known in the art. Additionally, the detection of a specific nucleic acid using a probe can be performed by contacting a sample nucleic acid with the probe under suitable conditions and then confirming the presence of the nucleic acid that hybridizes.
[0030] Methods for detecting specific nucleic acids using the probe or primer in the present invention include, for example but are not limited thereto, polymerase chain reaction (PCR), DNA sequencing, RT-PCR, primer extension method (Nikiforeov et al., Nucl Acids Res 22, 4167-4175, 1994), oligonucleotide extension analysis (Nickerson et al., Pro Nat Acad Sci USA, 87, 8923-8927, 1990), allele-specific PCR method (Rust et al., Nucl Acids Res, 6, 3623-3629, 1993), RNase mismatch cleavage (RNase mismatch cleavage, Myers et al., Science, 230, 1242-1246, 1985), and single strand conformation lymorphism (single strand conformation lymorphism, Orita et al., Pro Nat Acad Sci These include USA, 86, 2766-2770, 1989), simultaneous analysis of SSCP and heteroduplex (Lee et al., Mol Cells, 5:668-672, 1995), denaturation gradient gel electrophoresis (DGGE, Cariello et al., Am J Hum Genet, 42, 726-734, 1988), denaturation high-pressure liquid chromatography (Underhill et al., Genome Res, 7, 996-1005, 1997), hybridization reactions, DNA chips, etc. Examples of the above hybridization reactions include Northern hybridization (Maniatis T. et al., Molecular Cloning, Cold Spring Harbor Laboratory, NY, 1982), in situ hybridization (Jacquemier et al., Bull Cancer, 90:31-8, 2003), and microarray (Macgregor, Expert, Rev Mol Diagn 3:185-200, 2003) methods.
[0031] In addition, the present invention provides a kit for predicting the risk of developing open-angle glaucoma, comprising the above composition.
[0032] In the present invention, the kit may include a polynucleotide, primer, or probe for identifying one or more of the polymorphic markers, as well as one or more other component compositions, solutions, or devices suitable for the analysis method.
[0033] In the present invention, the kit may be a kit containing essential elements necessary to perform PCR. In addition to polynucleotides, primers, or probes specific to the polymorphic marker, the PCR kit may include a test tube or other suitable container, a reaction buffer (with varying pH and magnesium concentration), deoxynucleotides (dNTPs), enzymes such as Taq-polymerase and reverse transcriptase, DNase, RNAse inhibitors, DEPC-water, and sterile water. Effects of the invention
[0034] According to the present invention, there is an advantage that it can be usefully employed to predict the risk of developing open-angle glaucoma in Koreans based on single nucleotide polymorphisms. Brief explanation of the drawing
[0035] Figure 1 shows a histogram of the PRS divided by the median. Specific details for implementing the invention
[0036] Hereinafter, the present invention will be described in detail with reference to examples to aid in understanding. However, the following examples are merely illustrative of the content of the present invention and the scope of the present invention is not limited to the following examples. The examples of the present invention are provided to more completely explain the present invention to those with average knowledge in the art.
[0038] Example 1. Experimental Method
[0040] 1.1 Selection of Research Group
[0041] The study population was drawn from the KoGES (Korean Genome and Epidemiology Study) urban cohort (HEXA cohort, Health examinee cohort). The KoGES database, managed by the Korea Disease Control and Prevention Agency, currently contains genotyped data for all 58,700 participants using the Korean-chip microarray and Axiom Biobank version 1.1; phenotype information was also distributed to the Institute of Genomic Medicine at Seoul National University College of Medicine (Director: Professor Jong-il Kim). The KoGES DB has the advantage of being suitable for group studies as all participant information is anonymized, making it ethically uncontroversial as individuals cannot be tracked or identified based on phenotype or genotype data. Since the KoGES database included items regarding the presence or absence of glaucoma in participants, this information was utilized to distinguish between the patient and control groups, while the genotype information was used to calculate polygenic risk scores by extracting genotypes related to 19 SNPs. Among a total of 58,600 study participants with an average age of 53.8±8.0 years, 377 participants answered on the questionnaire that they had a history of glaucoma or a history of treatment.
[0043] 1.2 Sample Preparation and Allele Identification
[0045] Genomic DNA was isolated from blood using the MG Blood Genomic DNA Extraction SV kit (MGmed, Seoul, Korea). To extract genotype information from the KoGES DB, DNA was extracted from blood, and genotyping was performed using microarray sequencing (Korean Biobank Array version 1.1, Korean-chip). In this invention, 19 SNPs each at 19 loci for 19 species, including MIR4778 (19 species including rs2946370, see Table 1) were analyzed.
[0046] Genotyping analysis of 19 polymorphisms including rs2946370 was performed using the TaqMan SNP Genotyping Assay analysis IDs (Applied Biosystems, Foster City, CA) for C___2485201_10, C__11916555_30, C__15840320_10, and C___2485225_20, respectively, with the QuantStudio real-time polymerase chain reaction system (Applied Biosystems).
[0048] 1.3 Extraction of Independent Single Nucleotide Polymorphism (SNP) Factors
[0050] Based on three previous studies (Nature Communications, 2021, Gharahkhani / Nature Genetics, 2020, Craig / Nature Genetics, 2021, Sakaue), 19 independent SNPs of genome-wide significance were extracted from genome-wide association studies (GWAS) of glaucoma. Table 1 shows the 19 SNPs used in the construction of the PRS of the present invention.
[0052] No. rsID CHR POS(hg19) REF ALT OR BETA MAF P-value GENE (hg19) 1 rs2946370 2 66592411 C T 1.13 0.123 0.328 1.37.E-08 MIR4778Chr2:66,585,381-66,585,460(Sequence No. 1) 2 rs66500121 3 85137683 G A 1.12 0.113 0.174 2.30E-14 CADM2Chr3:85,008,140-86,123,579(Sequence No. 2) 3 rs4308305 3 171831116 C T 1.12 0.113 0.240 1.98E-09 FNDC3BChr3:171,757,368-172,119,459(Sequence No. 3) 4 rs9853115 3 186131600 A T 1.11 0.104 0.292 1.20.E-15 LINC02020Chr3:186,158,134-186,163,031(Sequence No. 4) 5 rs28795989 4 7891545 G A 1.15 0.140 0.180 2.80.E-25 AFAP1Chr4:7,760,440-7,941,588(Sequence No. 5) 6 rs61275591 5 55775556 G A 1.18 0.163 0.265 5.96.E-14 C5orf67Chr5:55,807,109-55,902,083(sequence number 6) 7 rs57111852 6 606263 A G 0.87 -0.139 0.185 8.50.E-13 EXOC2Chr6:485,154-693,139(Sequence No. 7) 8 rs2745572 6 1548369 G A 1.12 0.113 0.486 6.40.E-21 FOXC1Chr6:1,610,150-1,614,132(Sequence No. 8) 9 rs2526101 7 11677452 G A 0.90 -0.105 0.264 3.70.E-13 THSD7AChr7:11,409,992-11,871,824(Sequence No. 9) 10 rs1412829 9 22043926 G A 1.39 0.333 0.134 1.44E-27 CDKN2B-AS1Chr9:21,994,790-22,121,096(Sequence No. 10) 11 rs2472494 9 107695539 C T 1.20 0.185 0.457 1.11E-19 ABCA1Chr9:107,543,287-107,690,436(Sequence No. 11) 12 rs3829849 9 129390800 C T 0.84 -0.174 0.078 6.03E-09 LMX1BChr9:129,376,207-129,463,311(Sequence No. 12) 13 rs61870251 10 126284415 C A 0.87 -0.145 0.208 2.30E-10 LHPPChr10:126,150,392-126,302,710(Sequence No. 13) 14 rs11024102 11 17008605 C T 1.10 0.094 0.465 9.99E-09 PLEKHA7Chr11:16,798,844-17,035,961(Sequence No. 14) 15 rs4303192 11 47728924 C T 1.13 0.123 0.387 9.23E-09 AGBL2Chr11:47,681,143-47,736,921(Sequence No. 15) 16 rs58073046 11 120248493 G A 0.88 -0.128 0.170 1.30.E-14 ARHGEF12Chr11:120,207,122-120,360,646(Sequence No. 16) 17 rs35155027 14 61095174 C G 1.12 0.113 0.277 6.90.E-33 SIX1Chr14:61,110,139-61,116,195(Sequence No. 17) 18 rs150025731 15 74223501 A ACTCACCGG 1.14 0.130 0.439 3.07E-15 LOXL1Chr15:74,218,803-74,244,477(Sequence No. 18) 19 rs9913911 17 10031183 G A 0.91 -0.092 0.442 4.75E-08 GAS7Chr17:9,813,923-10,101,923(sequence number 19)
[0054] The odds ratio and minor allele frequency of each SNP were also extracted. Using open-angle glaucoma questionnaire data, the polygenic risk score (PRS) formula was applied to the KoGES city cohort (N=58,600). It was assumed that there is complete association equilibrium for SNPs that are far apart from each other, meaning that these SNPs are completely independent of one another. The polygenic risk score (PRS) was calculated for each individual in the KoGES database, and for verification, the prevalence of open-angle glaucoma was observed for each quintile (ranked from lowest to highest) of the PRS, and the age of each participant was also calculated.
[0056] Example 2. Experimental Results
[0058] The precision of the polygenic risk score was tested using quintiles of PRS from 1 (low) to 5 (high). The value obtained by dividing the PRS score by the median of the total PRS ranged from 0.16 to 5.61 (Fig. 1).
[0059] The PRS results based on the quintiles (N. in CA represents the number of patient cases) are shown in Table 2.
[0061] GRS5bin PRS Average Number of Cases Frequency of Cases Total Number 1 2.07096289 53 0.45221843 11720 2 2.860588022 62 0.529010239 11720 3 3.498454927 76 0.648464164 11720 4 4.262439959 73 0.622866894 11720 5 5.890287572 113 0.964163823 11720
[0062] GRS: Genetic risk score
[0063] PRS: Polygenc risk score
[0065] There were a total of 377 individuals diagnosed with pre-existing open-angle glaucoma. For each PRS quintile, the number of patients ranged from low PRS to high PRS to 53, 62, 76, 73, and 113 (Fig. 2).
[0067] GRS10bin GRSAverage Number of Cases Frequency of Cases Total Number 1 1.79609 23 0.392491 5860 2 2.345836 30 0.511945 5860 3 2.701569 27 0.460751 5860 4 3.019608 35 0.59727 5860 5 3.332795 38 0.648464 5860 6 3.664115 38 0.648464 5860 7 4.035477 33 0.56314 5860 8 4.489403 40 0.682594 5860 9 5.119029 47 0.802048 5860 10 6.661546 66 1.12628 5860
[0069] Meanwhile, the PRS results based on the deciles are shown in Table 3. A similar increasing pattern was derived from the PRS deciles (Fig. 3). This provided further validation for the newly established PRS. Among glaucoma patients, the average age of the 1st decile (lowest PRS) was 60.7 years, and the average age of the 5th decile (highest PRS) was 59.3 years.
[0070] Accordingly, a polygenetic risk score was derived based on 19 SNPs and the function of the PRS was verified in the KoGES cohort, confirming that the PRS of the present invention can be usefully used to determine the genetic risk of glaucoma.
[0072] Foregoing, specific parts of the present invention have been described in detail. It will be apparent to those skilled in the art that such specific descriptions are merely preferred embodiments and do not limit the scope of the invention. Accordingly, the actual scope of the invention is defined by the appended claims and their equivalents.
Claims
Claim 1 A method for providing information necessary for predicting the risk of developing open-angle glaucoma in Koreans, comprising the step of identifying all single nucleotide polymorphisms (SNPs) of rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731, and rs9913911 from a biological sample, method. Claim 2 In claim 1, the single nucleotide polymorphism (SNP) is located in the MIR4778 gene on chromosome 2 in the case of rs2946370, in the CADM2 gene on chromosome 3 in the case of rs66500121, in the FNDC3B gene on chromosome 3 in the case of rs4308305, in the LINC02020 gene on chromosome 3 in the case of rs9853115, in the AFAP1 gene on chromosome 4 in the case of rs28795989, in the C5orf67 gene on chromosome 5 in the case of rs61275591, in the EXOC2 gene on chromosome 6 in the case of rs57111852, in the FOXC1 gene on chromosome 6 in the case of rs2745572, and in the THSD7A gene on chromosome 7 in the case of rs2526101, In the case of rs1412829, it is located in the CDKN2B-AS1 gene on chromosome 9; in the case of rs2472494, it is located in the ABCA1 gene on chromosome 9; in the case of rs3829849, it is located in the LMX1B gene on chromosome 9; in the case of rs61870251, it is located in the LHPP gene on chromosome 10; in the case of rs11024102, it is located in the PLEKHA7 gene on chromosome 11; in the case of rs4303192, it is located in the AGBL2 gene on chromosome 11; in the case of rs58073046, it is located in the ARHGEF12 gene on chromosome 11; in the case of rs35155027, it is located in the SIX1 gene on chromosome 14; in the case of rs150025731, it is located in the LOXL1 gene on chromosome 15; and in the case of rs9913911, it is 17 A method characterized by being located in the GAS7 gene of a chromosome. Claim 3 A method according to claim 1, wherein the biological sample is selected from the group consisting of blood, tissue, cell, serum, plasma, saliva, and urine. Claim 4 A method according to claim 1, characterized in that the subject of the biological sample is a Korean. Claim 5 A biomarker composition for identifying open-angle glaucoma in Koreans comprising all single nucleotide polymorphisms (SNPs) of rs2946370, rs66500121, rs4308305, rs9853115, rs28795989, rs61275591, rs57111852, rs2745572, rs2526101, rs1412829, rs2472494, rs3829849, rs61870251, rs11024102, rs4303192, rs58073046, rs35155027, rs150025731 and rs9913911. Claim 6 A composition for predicting the risk of developing open-angle glaucoma, comprising a preparation capable of detecting the biomarker composition of claim 5. Claim 7 A kit for predicting the risk of developing open-angle glaucoma, comprising the composition of claim 6.
