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JP-2026514405-A - Methods and compositions for predicting and/or monitoring cardiovascular disease and for intervention thereof.

JP2026514405AJP 2026514405 AJP2026514405 AJP 2026514405AJP-2026514405-A

Abstract

This document describes methods and compositions for predicting cardiovascular disease (CVD). Specifically, this document describes methods and compositions for determining the methylation status of at least one CpG locus and the sequence of at least one single nucleotide polymorphism (SNP) to predict the detection of CVD or the estimation of survival from CVD.

Inventors

  • ドガン ミーシャンティニ ブイ．
  • ドガン ティムル ケイ．
  • フィリバート ロバート エー．

Assignees

  • カーディオ ダイアグノスティックス インコーポレイテッド

Dates

Publication Date
20260511
Application Date
20240329
Priority Date
20230330

Claims (20)

  1. A kit for determining the methylation status of at least one CpG dinucleotide and the genotype of at least one single nucleotide polymorphism (SNP), including the following: The first CpG dinucleotide of a GC locus selected from the group consisting of cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584, or At least one first nucleic acid primer, at least 8 nucleotides long, complementary to a bisulfite-converted nucleic acid sequence comprising a second CpG dinucleotide in linkage disequilibrium with a first CpG dinucleotide selected from the group consisting of cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584, wherein the linkage disequilibrium has a value of R > 0.3, and the at least one first nucleic acid primer detects a methylated CpG dinucleotide or an unmethylated CpG dinucleotide. Furthermore A first SNP selected from the group consisting of rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, or A first SNP selected from the group consisting of rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, and a second SNP in linkage disequilibrium. A second nucleic acid primer having a length of at least 8 nucleotides, complementary to the DNA sequence or the bisulfite-converted DNA sequence, wherein the linkage disequilibrium has a value of R > 0.3.
  2. The kit according to claim 1, wherein at least one first nucleic acid primer detects unmethylated CpG dinucleotides.
  3. The kit according to claim 1, wherein the at least one first nucleic acid primer detects methylated CpG dinucleotides.
  4. The kit according to any one of claims 1 to 3, wherein the at least one first nucleic acid primer comprises one or more nucleotide analogs.
  5. The kit according to any one of claims 1 to 4, wherein the at least one first nucleic acid primer comprises one or more synthetic or unnatural nucleotides.
  6. The kit according to any one of claims 1 to 5, further comprising a solid substrate bound to at least one first nucleic acid primer.
  7. The kit according to claim 6, wherein the substrate is a polymer, glass, semiconductor, paper, metal, gel, or hydrogel.
  8. The kit according to claim 6, wherein the solid substrate is a microarray or a microfluidic card.
  9. A kit according to any one of claims 1 to 8, further comprising a detectable label.
  10. The kit according to any one of claims 1 to 9, further comprising at least one third nucleic acid primer having a length of at least 8 nucleotides and being complementary to the nucleic acid sequence upstream of the CpG dinucleotide.
  11. The kit according to any one of claims 1 to 9, further comprising at least one third nucleic acid primer having a length of at least 8 nucleotides and being complementary to the nucleic acid sequence downstream of the CpG dinucleotide.
  12. A method for determining the presence of a biomarker in a biological sample derived from a subject, wherein the biomarker is related to detecting CVD, determining the severity of CVD, estimating survival from CVD, identifying, customizing, and/or optimizing interventions for CVD, managing CVD, and/or monitoring CVD, and the method is (a) A step of providing a first portion of the biological sample and a second portion of the biological sample, wherein at least nucleic acids derived from the first portion are bisulfite-converted; (b) The first portion of the biological sample The first CpG dinucleotide of a GC locus selected from the group consisting of cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584, or (c) Contacting a first oligonucleotide primer of at least 8 nucleotides in length with a sequence complementary to a second CpG dinucleotide in linkage disequilibrium with a first CpG dinucleotide selected from the group consisting of cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584, wherein the linkage disequilibrium has a value of R > 0.3, and the first nucleic acid primer detects methylated or unmethylated CpG dinucleotides; and (c) a second portion of the biological sample, A first SNP selected from the group consisting of rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, or A first SNP selected from the group consisting of rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, and a second SNP in linkage disequilibrium. A step comprising contacting the DNA sequence or the bisulfite-converted DNA sequence with a nucleic acid primer of at least 8 nucleotides length that is complementary to the DNA sequence, wherein the linkage disequilibrium has a value of R > 0.3, The percentage of methylation of a CpG dinucleotide at a GC locus selected from the group consisting of cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584, and the nucleotide identity of a first SNP selected from the group consisting of rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, or a second SNP in linkage disequilibrium with the first SNP, are biomarkers associated with detecting CVD or estimating survival from CVD. The aforementioned method.
  13. The method according to claim 12, wherein the biological sample is selected from the group consisting of blood and saliva.
  14. The method according to claim 12, wherein the at least one first nucleic acid primer detects unmethylated CpG dinucleotides.
  15. The method according to claim 12, wherein the at least one first nucleic acid primer detects a methylated CpG dinucleotide.
  16. The method according to claim 12, wherein the at least one first nucleic acid primer comprises one or more nucleotide analogs.
  17. The method according to claim 12, wherein the at least one first nucleic acid primer comprises one or more synthetic or unnatural nucleotides.
  18. The method according to claim 12, wherein the window for the incidence rate is 3 years.
  19. A method for determining the presence of a biomarker in a biological sample derived from a subject, wherein the biomarker is related to detecting CVD, determining the severity of CVD, estimating survival from CVD, identifying, customizing, and/or optimizing interventions for CVD, managing CVD, and/or monitoring CVD, and the method is (a) A step of obtaining nucleic acid samples from the target sample; (b) A step of performing a genotyping assay on a first portion of a nucleic acid sample in order to detect the presence of at least one SNP in order to obtain genotype data, The at least one SNP is A first SNP selected from rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433 or from Annex C, and/or A second SNP in linkage disequilibrium (R > 0.3) with a first SNP selected from rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433 or from Annex C, (c) a step of bisulfite-converting a nucleic acid in a second portion of the nucleic acid and performing a methylation evaluation on the second portion of the nucleic acid sample in order to detect the methylation status of at least one CpG site in order to obtain methylation data, The at least one CpG site is CpG sites selected from cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584 or from Annex A, and/or CpG sites that are collinear (R > 0.3) with CpGs selected from cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584 or from Annex A, The method comprising the steps of: (d) putting genotype data from step (b) and/or methylation data from step (c) into an algorithm that explains at least one SNP main effect and/or at least one CpG main effect and/or at least one interaction effect, wherein the algorithm is a machine learning algorithm capable of explaining linear and nonlinear effects.
  20. The method according to claim 19, wherein the at least one interaction effect is selected from the group consisting of gene-environment interaction (SNP × CpG) effects, gene-gene interaction (SNP × SNP) effects, and environment-environment interaction (CpG × CpG) effects.

Description

This disclosure relates, in general terms, to methods and compositions related to predicting cardiovascular disease (CVD) in individuals. Background Cardiovascular disease (CVD), particularly coronary heart disease (CHD), is the most common type of heart disease and was the cause of more than 360,000 deaths in the United States in 2017. To reduce these deaths, numerous risk estimators and detection methods have been developed to better identify people who have or are at risk of having CVD, including CHD. These tools, including the Framingham Risk Score (FRS) and, more recently, the ASCVD Pooled Cohort Equation (PCE), capture fluctuations in key physiological parameters known to be associated with the risk of CVD, including CHD, such as serum lipid levels. Similarly, methods such as stress echocardiography and computed tomography angiography (CCTA) are used for detection. Despite these considerable efforts, current risk estimators and detection tests often lack sensitivity and specificity, and are frequently impractical due to cost and the need to schedule in-person consultations that can take several weeks. Furthermore, some current risk estimators and detection methods, such as catheterization, can have serious side effects, including stroke and heart attack. Consequently, there is a need for alternative stratification, detection, and management approaches for CVD that offer minimal risk, scalability, and a viable outlook. Overview Methods and compositions are provided for predicting the presence and/or severity (e.g., level of occlusion) of cardiovascular disease (CVD), and for managing, monitoring, and/or treating CVD. For example, methods and compositions for predicting coronary heart disease (CHD) are described herein. General principles apply to incidence windows (e.g., 1 month, 6 months, 2 years, or 10 years), as well as the incidence, prevalence, or severity of other types of CVD, non-limitingly including CHD, stroke, arrhythmia, cardiac arrest, and congestive heart failure. The same general principles also apply to survival from CVD or CVD events, as well as to the management of CVD or CVD events, including, but not limited to, identifying, customizing, and optimizing lifestyle (e.g., exercise, diet) and/or therapeutic interventions (e.g., specific drugs or combinations thereof) and/or medical interventions (e.g., stent placement, angioplasty). The same general principles also apply to monitoring CVD or CVD events, the severity of CVD or CVD events, and/or responses to lifestyle, therapeutic interventions, and/or medical interventions. Specifically, methods and compositions comprising determining the methylation status of at least one CpG locus and/or at least one single nucleotide polymorphism (SNP) are described. A kit is provided for determining the methylation status of at least one CpG dinucleotide and/or the genotype of at least one single nucleotide polymorphism (SNP) in one context. Such a kit typically involves determining the first CpG dinucleotide of a GC locus selected from the group consisting of cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584, or from cg04988978, cg21161138, cg12655112, cg03725309, cg12586707, and cg17901584. A bisulfite-converted nucleic acid sequence comprising a bisulfite-converted nucleic acid sequence containing a 2 CpG dinucleotide in linkage disequilibrium with a 1 CpG dinucleotide of a GC locus selected from the group, wherein the linkage disequilibrium has a value of R > 0.3, and the at least one 1 nucleic acid primer detects methylated or unmethylated CpG dinucleotides. A first nucleic acid primer, and/or a first SNP selected from the group consisting of rs2869675, rs4376434, rs12129789, rs7585056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, or rs2869675, rs4376434, rs12129789, rs7585 The present invention comprises at least one second nucleic acid primer, at least 8 nucleotides long, complementary to the DNA sequence of a second SNP in linkage disequilibrium with a first SNP selected from the group consisting of 056, rs710987, rs4639796, rs1333048, rs12714414, rs942317, and rs1441433, wherein the linkage disequilibrium has a value of R > 0.3. In some embodiments, at least one first nucleic acid primer detects unmethylated CpG dinucleotides. In some embodiments, at least one first nucleic acid primer detects methylated CpG dinucleotides. In some embodiments, the kit described herein further comprises at least one third nucleic acid primer having a length of at least 8 nucleotides and being complementary to the nucleic acid sequence upstream of the CpG dinucleotide. In some embodiments, the kit further comprises at least one third nucleic acid primer having a length of at least 8 nucleotides and being complementary to the nucleic acid sequence downstream of the CpG dinucleotide. In some embodiments, at least one first nucleic acid primer comprises one or more nucleotide analogs. In some embodiments, at least