Single nucleotide polymorphism marker associated with reduction in rey complex figure copy score for predicting risk of developing alzheimer's disease and use thereof

Abstract

The present invention relates to: a method for providing information which can diagnose early and predict groups with the risk of developing Alzheimer's disease by providing SNP markers capable of predicting a high risk of developing Alzheimer's disease in Koreans; a composition for predicting the risk of developing Alzheimer's disease; and a microarray and a kit, each comprising same.

Description

Single nucleotide polymorphism markers associated with reduced Ley complexity copy score for predicting risk of developing Alzheimer's disease and their use

[0001] The present invention relates to a method for predicting the risk of developing Alzheimer's disease by identifying a specific single nucleotide polymorphism (SNP) that has a significant correlation with the risk of developing Alzheimer's disease, a composition for predicting the risk of developing Alzheimer's disease comprising a polynucleotide, polypeptide, antibody or cDNA capable of identifying the SNP, and a microarray and kit comprising the same.

[0002] In South Korea, it's estimated that approximately 10% of the population aged 65 and older suffer from dementia, and as the population ages, the personal and societal burden of dementia is increasing. The prevalence of dementia doubles every five years after age 65, and South Korea is projected to become the country with the fastest-growing dementia population in the world. Approximately 60 to 70% of dementia cases in Korea and abroad are due to Alzheimer's disease, a condition for which there is currently no known underlying cause or treatment.

[0003] Alzheimer's disease is a progressive disorder that causes cognitive impairment and memory loss. Major risk factors for Alzheimer's disease include age, family history, and lifestyle. Alzheimer's disease involves a chronic, progressive process leading to neurodegeneration, including axonal damage, cell death, and gliosis. The pathogenesis and pathophysiology of neurodegenerative diseases are complex and only a small part of the underlying cause is understood.

[0004] In humans, there is a mutation at a frequency of about 1 per 1,000 bases, which is called a single nucleotide polymorphism (SNP). A 5% polymorphism is called a common polymorphism, and a 1 to 5% polymorphism is called a rare polymorphism. Currently, many experimental techniques have been developed to analyze the entire base sequence of a human, and among them, genome-wide association study (GWAS) is currently being used to study many diseases. In relation to Alzheimer's disease, genome-wide association study (GWAS) has discovered more than 30 independent genetic loci, but more than half of the phenotypic variation still remains unexplained.

[0005] Meanwhile, the Rey Complex Figure Test (RCFT) assesses visual memory / visual-spatial abilities. It can measure imitation time, imitation score, immediate recall, delayed recall, true positives, false positives, positive positives, recognition index, and nonspecific recognition errors.

[0006] Against this backdrop, the inventors of the present invention have made extensive research efforts to develop a technique that can more effectively predict the onset of Alzheimer's dementia.

[0007] As a result, the inventors of the present invention identified a variant of SNP that indicates the risk of developing Alzheimer's disease, confirmed that the decline in the Rayleigh complex shape test was greater in the presence of such a variant, and developed a method for providing information that can evaluate the possibility of developing Alzheimer's dementia in an individual, thereby completing the present invention.

[0008] The purpose of the present invention is to provide a method for predicting the risk of developing Alzheimer's disease by identifying specific SNPs that have a significant correlation with the risk of Alzheimer's disease in a genetic sample obtained from a patient.

[0009] Another object of the present invention is to provide a method for providing information for predicting the risk of developing Alzheimer's disease by identifying specific SNPs that have a significant correlation with the risk of Alzheimer's disease in a genetic sample obtained from a patient.

[0010] Another object of the present invention is to provide a microarray for predicting the risk of developing Alzheimer's disease, comprising a polynucleotide, a polypeptide, an antibody therefor, or a cDNA thereof capable of identifying a specific SNP marker.

[0011] Another object of the present invention is to provide a kit for predicting the risk of developing Alzheimer's disease, comprising a polynucleotide, polypeptide, antibody therefor, or cDNA thereof capable of identifying a specific SNP marker.

[0012] Against this backdrop, the inventors of the present invention have made extensive research efforts to develop a technique that can more effectively predict the onset of Alzheimer's dementia.

[0013] As a result, the inventors of the present invention confirmed that the decrease in the copy score of the Rey Complex Figure Test was greater when a single nucleotide polymorphism (SNP) that specifically appears in the onset of Alzheimer's disease was expressed, utilizing the genome-wide association study (GWAS) methodology, and completed the present invention.

[0014] Hereinafter, the configuration of the present invention will be described in detail.

[0015] One aspect of the present invention relates to a genetic sample obtained from a patient,

[0016] A method for providing information for predicting the risk of developing Alzheimer's disease is provided, comprising the step of identifying a single nucleotide polymorphism (SNP) represented by rs150908390.

[0017] The above genetic sample refers to DNA or RNA that can be isolated from any cell of the subject (patient), including blood, skin cells, mucosal cells, and hair. The method for extracting DNA or RNA from the cells is not particularly limited, and any technique known in the art or a commercially available DNA or RNA extraction kit can be used.

[0018] The subject (patient) above may include a subject diagnosed with or suspected of having Alzheimer's disease. The subject may be a vertebrate, mammal, amphibian, reptile, bird, etc., and may specifically be a mammal. For example, the subject may be a human (Homo sapiens).

[0019] In the present invention, the term "gene" may be used interchangeably with the terms "polynucleotide" and "nucleic acid." The term "gene" refers to a DNA segment involved in the production of a polypeptide chain, and may include regions preceding and following a coding region, such as a promoter and a 3'-untranslated region, as well as intervening sequences (introns) between individual coding segments (exons).

[0020] The term "genetic polymorphism" used herein refers to a case where two or more alleles exist at a single genetic locus, and a case where a genetic variation occurs at a frequency of at least 1% or more in a population. Genetic polymorphism and mutation are distinguished, and genetic polymorphism refers to a case where a genetic variation shows a frequency of at least 1% or more in a population, and a genetic variation found at a frequency lower than 1% is collectively called a mutation. An insertion, deletion, or substitution of a single nucleotide in DNA is called a single nucleotide polymorphism (SNP).

[0021] In this specification, "single nucleotide polymorphism (SNP)" refers to a variation in DNA sequence that occurs when a single base (A, T, C, or G) in the genome differs between members of a species or between pairs of chromosomes of an individual. For example, in a certain region of the DNA chain, some people have adenine (A), while others have cytosine (C). These slight differences (SNPs) can alter the function of each gene, and these interact to create different individuals and differences in susceptibility to different diseases. In general, almost all SNPs have two alleles. Within a population, a SNP can be assigned a minor allele frequency (MAF; the lowest allele frequency at a locus found in a particular population). A single nucleotide can be changed (substituted), removed (deleted), or added (inserted) to a polynucleotide sequence. SNPs can cause a change in the translation frame.

[0022] Meanwhile, when indicating a mutation of a gene in this specification, [base letter / base letter] means that the base letter written on the left is replaced with the base letter written on the right.

[0023] As used herein, “polynucleotide” or “nucleic acid” refers to deoxyribonucleotides (DNA) or ribonucleotides (RNA) in single- or double-stranded form. Unless otherwise specified, known analogs of naturally occurring nucleotides that hybridize to nucleic acids in a manner similar to naturally occurring nucleotides are also included. DNA is generally composed of four bases: adenine (A), guanine (G), cytosine (C), and thymine (T), while RNA has uracil (U) instead of thymine. In a nucleic acid double strand, A forms hydrogen bonds with T or U, and C forms hydrogen bonds with G, and this relationship between bases is called “complementary.” Meanwhile, in this specification, unless otherwise stated, 'polynucleotide' means a polynucleotide having a contiguous base sequence of 8 to 100 bases including the SNP of the present invention in the genomic region where the SNP is located.

[0024] In the present invention, when a substitution of the base represented by rs150908390 occurs, it can be predicted that the risk of developing Alzheimer's disease is higher when the base sequence is G than when it is A.

[0025] In this specification, “genomic DNA (gDNA)” means DNA that contains almost complete genetic information, which is the total base sequence of the genes of an individual.

[0026] In the present invention, “risk of onset” or “likelihood of onset” may mean the relative risk of onset of Alzheimer’s disease, and specifically may mean the likelihood of progressing to Alzheimer’s disease.

[0027] In the present invention, “prediction” may mean not only determining the possibility of developing Alzheimer’s disease by confirming the presence or characteristics of a pathological condition, but also determining whether there is drug responsiveness, resistance, etc. after Alzheimer’s disease treatment.

[0028] In the present invention, the above information providing method can be usefully utilized to predict the risk of developing Alzheimer's disease in Koreans.

[0029] In the present invention, the fact that the single nucleotide polymorphism marker can be used to predict the risk of developing Alzheimer's disease is based on the fact that the genetic analysis results of a group that developed Alzheimer's disease showed a high probability of the presence of a specific base at a single nucleotide polymorphism site.

[0030] Another aspect of the present invention is a composition for predicting the risk of developing Alzheimer's disease, comprising a polynucleotide consisting of 10 or more consecutive bases including a single nucleotide polymorphism (SNP) represented by rs150908390 or a polynucleotide that specifically hybridizes with its complementary polynucleotide.

[0031] The polynucleotide composed of 10 or more consecutive bases according to the present invention or its complementary polynucleotide may include a polynucleotide composed of 10 or more consecutive bases, preferably 10 to 100, more preferably 20 to 80, and even more preferably 40 to 60, or a polynucleotide that specifically hybridizes with the polynucleotide or its complementary polynucleotide, but is not limited thereto.

[0032] In the above composition, the polynucleotide that specifically hybridizes with the polynucleotide described above may be a probe or a primer.

[0033] In the present invention, “primer” refers to an oligonucleotide, which can act as an initiation point for synthesis under conditions that induce the synthesis of a primer extension product complementary to a nucleic acid chain (template), i.e., the presence of nucleotides and a polymerization agent such as DNA polymerase, and conditions of suitable temperature and pH. Preferably, the primer is a deoxyribonucleotide and may be single-stranded. The primer used in the present invention may include naturally occurring dNMPs (i.e., dAMP, dGMP, dCMP, and dTMP), modified nucleotides, or non-natural nucleotides. In addition, the primer may also include ribonucleotides.

[0034] In the present invention, "probe" refers to a linear oligomer having a natural or modified monomer or linkage comprising deoxyribonucleotides and ribonucleotides capable of hybridizing to a specific nucleotide sequence. Preferably, the probe may be single-stranded for maximum efficiency in hybridization. The probe may preferably be a deoxyribonucleotide.

[0035] As a probe used in the present invention, a sequence perfectly complementary to the sequence including the SNP may be used, but a substantially complementary sequence may also be used as long as it does not interfere with specific hybridization. Preferably, a probe not used in the present invention includes a sequence capable of hybridizing to a sequence including 10 to 30 consecutive nucleotide residues including the SNP of the present invention. More preferably, the 3' end or 5' end of the probe may have a base complementary to the SNP base. In general, since the stability of a duplex formed by hybridization tends to be determined by the identity of the terminal sequence, if the terminal portion of a probe having a base complementary to the SNP base at the 3' end or 5' end does not hybridize, such a duplex may be disassembled under stringent conditions.

[0036] In addition, the present invention provides a composition for predicting the risk of developing Alzheimer's disease, comprising a polypeptide encoded by the polynucleotide or an antibody specific therefor.

[0037] In the present invention, the process may begin with a step of amplifying or hybridizing a polymorphic site corresponding to the sequence represented by rs150908390 with a probe. Any method known in the art can be used for the step of amplifying or hybridizing the polymorphic site with a probe. For example, the method may be a method of amplifying a target nucleic acid via PCR and purifying it. In addition, the above method may be used, such as ligase chain reaction (LCR) (Wu and Wallace, Genomics 4, 560 (1989), Landegren et al., Science 241, 1077 (1988)), transcription amplication (Kwoh et al., Proc. Natl. Acad. Sci. USA 86, 1173 (1989)), self-sustaining sequence replication (Guatelli et al., Proc. Natl. Acad. Sci. USA 87, 1874 (1990)), or nucleic acid-based sequence amplification (NASBA).

[0038] In addition, the step of confirming the presence or absence of the mutation includes, but is not limited to, sequence analysis, hybridization by microarray, allele specific PCR, dynamic allele specific hybridization (DASH), PCR extension analysis, SSCP, PCR-RFLP analysis or TaqMan technique, SNPlex platform (Applied Biosystems), mass spectrometry (e.g., Sequenom's MassARRAY system), mini-sequencing method, Bio-Plex system (BioRad), CEQ and SNPstream system (Beckman), Molecular Inversion Probe array technology (e.g., Affymetrix GeneChip), and BreadArray technology (e.g., Illumina GoldenGate and Infinium assays). One or more alleles of a polymorphic marker, including a microsatellite, SNP, or other type of polymorphic marker, can be identified using the above methods or other methods available to those skilled in the art to which the present invention pertains. Determining the base pairs of such polymorphic sites can preferably be performed using a SNP chip.

[0039] In addition, in the step of confirming the genotype, gene sequence analysis can be performed. The sequence analysis can be performed using any method known in the art. For example, the sequence analysis can be performed using an automatic sequencer, or can be performed by at least one method selected from known methods such as pyrosequencing, PCR-RELP (restriction fragment length polymorphism), PCR-SSCP (single strand conformation polymorphism), PCR-SSO (specific sequence oligonucleotide), ASO (allele specific oligonucleotide) hybridization combining PCR-SSO and dot hybridization, TaqMan-PCR, MALDI-TOF / MS, RCA (rolling circle amplification), HRM (high resolution melting), primer extension, Southern blot hybridization, or dot hybridization.

[0040] Another aspect of the present invention is a microarray for predicting the risk of developing Alzheimer's disease, comprising: a polynucleotide consisting of 10 or more consecutive bases including a single nucleotide polymorphism (SNP) represented by rs150908390 or a complementary polynucleotide thereof; a polynucleotide hybridizing therewith; a polypeptide encoded thereby; an antibody specific therefor; or cDNA of the polypeptide.

[0041] In addition, the present invention provides a microarray for predicting the risk of developing Alzheimer's disease, comprising the polynucleotide, a polynucleotide hybridizing therewith, a polypeptide encoded thereby, an antibody specific therefor, or cDNA of the polypeptide.

[0042] A microarray according to the present invention may comprise DNA or RNA polynucleotides. The microarray may be a conventional microarray, except that the probe polynucleotide comprises the polynucleotide of the present invention. Methods for manufacturing a microarray by immobilizing the probe polynucleotide on a substrate are well known in the art. The probe polynucleotide refers to a hybridizable polynucleotide, and refers to an oligonucleotide capable of sequence-specific binding to complementary strands of nucleic acids. The probe of the present invention is an allele-specific probe, which means that a polymorphic site exists in nucleic acid fragments derived from two members of the same species, and thus hybridizes to a DNA fragment derived from one member but not to a fragment derived from the other member. In this case, the hybridization conditions must be sufficiently stringent to ensure that the probe exhibits a significant difference in hybridization intensity between alleles and hybridizes to only one of the alleles. This can induce a favorable hybridization difference between different allelic forms. The above diagnostic methods include detection methods based on nucleic acid hybridization, such as Southern blot, and in methods using DNA chips, the detection method may be provided in a form pre-bound to the DNA chip substrate. The above hybridization can usually be performed under stringent conditions, such as a salt concentration of 1 M or less and a temperature of 25°C or higher.

[0043] In the present invention, the term "antibody" refers to a specific protein molecule directed against an antigenic site, a term well known in the art. For the purposes of the present invention, the antibody refers to an antibody that specifically binds to a polypeptide comprising the SNP marker of the present invention. Such antibodies can be produced by conventional methods, such as cloning each gene into an expression vector to obtain a protein encoded by the marker gene, and producing the obtained protein using conventional methods. This also includes partial peptides that can be produced from the protein, and the partial peptides of the present invention include at least 7 amino acids, preferably 9 amino acids, and more preferably 12 or more amino acids. The form of the antibody of the present invention is not particularly limited, and polyclonal antibodies, monoclonal antibodies, or any antibody having antigen binding properties, as well as portions thereof, can be included in the antibody of the present invention, and all immunoglobulin antibodies can be included. Furthermore, the antibody of the present invention can also include specialized antibodies, such as humanized antibodies. The antibody used for detecting the marker for predicting the risk of developing Alzheimer's disease of the present invention may include a complete form having two full-length light chains and two full-length heavy chains, as well as a functional fragment of the antibody molecule. A functional fragment of an antibody molecule means a fragment that possesses at least an antigen-binding function, and may be Fab, F(ab'), F(ab')2, or Fv.

[0044] Another aspect of the present invention is a kit for predicting the risk of developing Alzheimer's disease, comprising: a polynucleotide consisting of 10 or more consecutive bases including a single nucleotide polymorphism (SNP) represented by rs150908390 or a complementary polynucleotide thereof; a polynucleotide hybridizing therewith; a polypeptide encoded thereby; an antibody specific therefor; or cDNA of the polypeptide.

[0045] In addition, the present invention provides a kit for predicting the risk of developing Alzheimer's disease, comprising the polynucleotide, a polynucleotide hybridizing therewith, a polypeptide encoded thereby, an antibody specific therefor, or cDNA of the polypeptide.

[0046] In the present invention, the kit may be, but is not limited to, a DNA chip, an RT-PCR kit, or a protein chip kit.

[0047] The above kit can predict the risk of developing Alzheimer's disease by confirming through amplification of a SNP polymorphism marker, which is a marker for predicting the risk of developing Alzheimer's disease, or by confirming the expression level of the SNP polymorphism marker at the level of DNA or mRNA. For example, in the present invention, the kit for measuring the mRNA expression level of the marker for predicting the risk of developing Alzheimer's disease may be a kit including essential elements required for performing RT-PCR. In addition to each primer pair specific for the gene of the marker for predicting the risk of developing Alzheimer's disease, the RT-PCR kit may include a test tube or other appropriate container, a reaction buffer (with various pH and magnesium concentrations), deoxynucleotides (dNTPs), an enzyme such as Taq polymerase and reverse transcriptase, DNase, RNase inhibitor, DEPC water, sterile water, etc. In addition, it may include a primer pair specific for a gene used as a quantitative control. In addition, preferably, the kit according to the present invention may be a kit for predicting the risk of developing Alzheimer's disease, which includes the essential elements necessary for performing a DNA chip. The DNA chip kit is a tool in which nucleic acid species are attached in a gridded array on a flat solid support, typically a glass surface no larger than a microscope slide, so that the nucleic acids are uniformly arranged on the chip surface, thereby allowing multiple hybridization reactions to occur between the nucleic acids on the DNA chip and complementary nucleic acids contained in a solution treated on the chip surface, thereby enabling massive parallel analysis. In addition, the kit according to the present invention may be a protein chip kit. The protein chip kit can measure the expression level of a protein composed of a mutated amino acid sequence. The protein chip kit may include a substrate for immunological detection of an antibody, an appropriate buffer solution, a secondary antibody labeled with a chromogenic enzyme or fluorescent substance, a chromogenic substrate, etc.Peroxidase, alkaline phosphatase, etc. can be used as chromogenic enzymes. In addition, FITC, RITC, etc. can be used as fluorescent substances, and AVTS (2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid)), OPD (o-phenylenediamine), TMB (tetramethyl benzidine), etc. can be used as chromogenic substrates.

[0048] The kit of the present invention, manufactured as described above, is very economical compared to conventional general genetic mutation detection methods, as it saves time and money. Using conventional genetic mutation detection methods such as SSCP (Single Strand Conformational Polymorphism), PTT (Protein Truncation Test), cloning, and direct sequencing, it takes several days to several months on average to test all genes. In addition, next generation sequencing (NGS) can also be used to precisely test genetic mutations quickly and simply. When testing for mutations using conventional analysis methods such as SSCP, cloning, direct sequencing, and RFLP (Restriction Fragment Length Polymorphism), it takes about a month to complete the test, whereas using the kit of the present invention, if sample DNA is prepared, results can be obtained in about 10 to 11 hours, and since a set of primers capable of detecting mutations is integrated into a single chip, not only time but also cost can be saved compared to conventional methods. Since the average reagent cost per experiment is less than half that of conventional methods, even greater cost savings can be expected when considering the researcher's labor costs.

[0049] The advantages and features of the present invention, and the methods for achieving them, will become clearer with reference to the embodiments described in detail below. However, the present invention is not limited to the embodiments disclosed below, but may be implemented in various different forms. These embodiments are provided solely to ensure that the disclosure of the present invention is complete and to fully inform those skilled in the art of the scope of the invention. The present invention is defined solely by the scope of the claims.

[0050] The present invention relates to a set of SNP genes, a composition, a method for providing information, and a kit capable of predicting the risk of developing Alzheimer's disease. SNP variations associated with the risk of developing Alzheimer's disease were identified through genome-wide association analysis (GWAS), and the SNP variations can be utilized to diagnose or predict the onset of Alzheimer's disease in Koreans.

[0051] Figure 1 is a graph showing the Manhattan plot results for SNPs associated with Alzheimer's disease.

[0052] Figure 2 is a graph showing a regional plot of rs150908390, which is located on chromosome 11 and between the DDX10 gene and C110rf87.

[0053] Figure 3 is a mean profile plot graph showing the copy score measured over time for rs150908390.

[0054] Figure 4 is a survival curve analyzing the effect of the rs150908390 mutation and the onset of Alzheimer's disease over time.

[0055] The advantages and features of the present invention, and the methods for achieving them, will become clearer with reference to the embodiments described in detail below together with the accompanying drawings. However, the present invention is not limited to the embodiments disclosed below, but may be implemented in various different forms. These embodiments are provided solely to ensure that the disclosure of the present invention is complete and to fully inform those skilled in the art of the scope of the invention, and the present invention is defined solely by the scope of the claims.

[0056]

[0057] Example 1. Whole-genome correlation analysis study

[0058] The study sample included 1,325 subjects enrolled in cohorts at Chosun University and Chonnam National University who had completed the Rey Complex Figure Test at least twice. Clinical diagnosis of Alzheimer's disease (AD) status was made according to the NINCDS-ADRDA (National Institute of Neurological and Communicative Disorders and Stroke-Alzheimer Disease and Research Disorders Association) criteria. Cognitively normal (CN) subjects had no evidence of neurological disease or impairment in cognitive function or activities of daily living. Subjects with a history of brain MRI, head trauma, or a history of psychiatric disorders that could affect mental function were excluded. At baseline, there were 50 cognitively normal (CN) subjects, 432 subjects with mild cognitive impairment (MCI), and 43 subjects with Alzheimer's disease (AD). The final sample included 775 controls.

[0059] The research protocol was approved by the Chosun University Review Board (CHOSUN 2013-12-018-068) and the Chonnam National University Review Board (CNUH?2019?279). All volunteers or authorized guardians of individuals with cognitive impairment provided written consent prior to participation.

[0060] And to determine which genes influence cognitive decline, a linear mixed model (LMM) was used.

[0061] 1-1. Manhattan Plot Verification

[0062] Manhattan plots are used to identify and display statistically significant SNPs in GWAS. The x-axis of the Manhattan plot is a scatter plot visualizing the statistical value, or p-value, of each SNP according to its location in the genome. If an association with a phenotype is observed, SNPs that show significance above or near the threshold at the locus may appear in clusters. In the genome-wide analysis results, the p-value is 5x10 -8 Below (above the red line, p-value < 5x10 -8 ) was identified, and it can be interpreted that this SNP has statistical significance (Fig. 1).

[0063] 1-2. Whole genome correlation analysis

[0064] We conducted a correlation analysis between Alzheimer's disease and whole-genome sequencing. Copy is a test designed to measure spatiotemporal function, and spatiotemporal function is closely related to Alzheimer's disease. Therefore, the Rey Complex Figure Test copy score was used as the dependent variable. We focused on the effects of SNPs and their interaction terms (the interaction between SNPs and time from baseline), and considered age at baseline, sex, education, years, Principal Components (PCs) 1 to 10, and time from baseline as variables. Each model for each subject i was set up as follows:

[0065] [Calculation Formula 1]

[0066]

[0067] Y_ij: jth copy score of the ith subject

[0068] age_i: Age of the i-th subject

[0069] education_i: Years of education of the i-th subject

[0070] PC_ik: kth PC score of the ith subject

[0071] t_ij: jth observation of the ith subject (t_i0=0, t_i1=1 .. )

[0072] G_i: SNP of the Ith subject

[0073] e_ij: error term

[0074] beta: Regression coefficient of fixed effects

[0075] b: Regression coefficient of the variance effect

[0076] We applied the relevant reference panel (GRCh37.p13) generated by the GenomeAsia 100K project supported by the National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health (NIH).

[0077] Dependent variable, chromosomal location, MAF, single nucleotide polymorphism, regression coefficient, error, significance probability, gene, RCFT, copy score, 111091212310.027, rs1509083902.00.281.1e-12, DDX10, C11orf87

[0078]

[0079] As a result of the analysis, the verified SNP was rs150908390, and the regional plot showed that it was located on chromosome 11, between the DDX10 gene and C110rf87, and the location was 109121231 based on GRCh37.p13 (109250504 based on GRCh38.p14) (Fig. 2).

[0080] On the graph, the x-axis represents the time (years) from one measurement to the next, and the y-axis represents the copy score. The decline in RCFT copy score was significantly greater in subjects with the rs150908390 variant (Carrier, red on the graph) than in subjects without the variant (Non-Carrier, light blue on the graph) (Fig. 3). In addition, rs150908390 analyzed using the NIH reference panel (GRCh37.p13) was confirmed to have the A genotype as the majority allele and the G genotype as the minor allele, and the frequency of the minor allele (maf) was 0.027.

[0081] Through this, we were able to verify the accuracy of statistical significance confirmed by whole genome sequencing.

[0082]

[0083] Example 2. Survival Analysis Verification

[0084] We analyzed the incidence of Alzheimer's disease over time when rs150908390, a mutation validated in genome-wide correlation analysis, was mutated. For this analysis, we performed Cox regression, a predictive model for time-to-event data, and the Kaplan-Meier method, which estimates conditional probabilities at each time point of an event and calculates the product of these probabilities to estimate survival rates at each time point.

[0085] The analysis results showed that the group with the rs150908390 mutation (red line) had a significantly shorter time from the first observation to the onset of Alzheimer's disease compared to the group without the mutation (light blue line) (Figure 4). This suggests that the rs150908390 mutation significantly influences the onset of Alzheimer's disease.

Claims

1. Regarding genetic samples obtained from patients, A method for providing information for predicting the risk of developing Alzheimer's disease, comprising the step of identifying a single nucleotide polymorphism (SNP) represented by rs150908390.

2. In paragraph 1, A method for providing information for predicting the risk of developing Alzheimer's disease, wherein when a substitution of the base indicated by the above rs150908390 occurs, the risk of developing Alzheimer's disease is predicted to be higher when the base sequence is G than when it is A. A composition for predicting the risk of developing Alzheimer's disease, comprising a polynucleotide consisting of 10 or more consecutive bases including a single nucleotide polymorphism (SNP) represented by rs150908390 or a polynucleotide that specifically hybridizes with its complementary polynucleotide.

4. In paragraph 3, A composition for predicting the risk of developing Alzheimer's disease, wherein the polynucleotide that specifically hybridizes above is a probe or primer.

5. A microarray for predicting the risk of developing Alzheimer's disease, comprising a polynucleotide consisting of 10 or more consecutive bases including a single nucleotide polymorphism (SNP) represented by rs150908390 or a complementary polynucleotide thereof; a polynucleotide hybridizing therewith; a polypeptide encoded thereby; an antibody specific therefor; or cDNA of the polypeptide.

6. A kit for predicting the risk of developing Alzheimer's disease, comprising: a polynucleotide consisting of 10 or more consecutive bases including a single nucleotide polymorphism (SNP) represented by rs150908390, or a complementary polynucleotide thereof; a polynucleotide hybridizing therewith; a polypeptide encoded thereby; an antibody specific therefor; or cDNA of the polypeptide.

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