Genes and polymorphisms associated with cardiovascular disease and their use

• US 20030224418A1
• Filed: 03/27/2003
• Published: 12/04/2003
• Est. Priority Date: 03/09/2001
• Status: Abandoned Application

• Current Assignee: Sequenom-Gemini Limited
• Original Assignee: Sequenom-Gemini Limited
• Inventors: Braun, Andreas, Bansal, Aruna, Kleyn, Patrick W.
• Application Number:
  US10/403,902
• Publication Number:
  US 20030224418A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Genes and polymorphisms associated with cardiovascular disease, methods that use the polymorphism to detect a predisposition to developing high cholesterol, low HDL or cardiovascular disease, to profile the response of subjects to therapeutic drugs and to develop therapeutic drugs are provided.

Claims

1. A method for detecting the presence or absence in a subject of at least one allelic variant of a polymorphic region of a gene associated with cardiovascular disease, comprising:

the step of detecting the presence or absence of an allelic variant of a polymorphic region of a cytochrome C oxidase subunit VIb (COX6B) gene of the subject that is associated with high serum cholesterol or an allelic variant of a polymorphic region of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene of the subject that is associated with low serum high density lipoprotein (HDL).

2. The method of claim 1, wherein the allelic variant is of a polymorphic region of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

3. The method of claim 1, further comprising detecting the presence or absence in a subject of least one allelic variant of another gene associated with cardiovascular disease.

4. The method of claim 3, wherein the other gene is selected from the group consisting of cholesterol ester transfer protein, plasma (CETP);

apolipoprotein A-IV (APO A4);

apolipoprotein A-I (APO A1);

apolipoprotein E (APO E);

apolipoprotein B (APO B);

apolipoprotein C-III (APO C3);

a gene encoding lipoprotein lipase (LPL);

ATP-binding cassette transporter (ABC

     1);

paraoxonase 1 (PON

     1);

paraoxonase 2 (PON

     2);

5,10-methylenetetrahydrofolate r reductase (MTHFR);

a gene encoding hepatic lipase, E-selectin, G protein beta 3 subunit and angiotensin II type 1 receptor gene.

5. The method of claim 2, wherein the polymorphic region is a single nucleotide polymorphism (SNP).

6. The method of claim 5, wherein the SNP is at position 2577 of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene sequence and the allelic variant is represented by an A nucleotide in the sense strand or a T nucleotide in the corresponding position in the antisense strand.

7. The method of claim 1, wherein the detecting step is by a method selected from the group consisting of allele specific hybridization, primer specific extension, oligonucleotide ligation assay, restriction enzyme site analysis and single-stranded conformation polymorphism analysis.

8. The method of claim 6, further comprising:

(a) hybridizing a target nucleic acid comprising a N-acetylglucosaminyl transferase component GPI-1 (GPI-1)-encoding nucleic acid or fragment thereof with a nucleic acid primer that hybridizes adjacent to nucleotide 2577 of the GPI-1 gene;

(b) extending the nucleic acid primer using the target nucleic acid as a template; and

(c) determining the mass of the extended primer to identify the nucleotide present at position 2577, thereby determining the presence or absence of the allelic variant.

9. The method of claim 1, wherein the detecting step comprises mass spectrometry.

10. The method of claim 1, wherein the detecting step utilizes a signal moiety selected from the group consisting of:

radioisotopes, enzymes, antigens, antibodies, spectrophotometric reagents, chemiluminescent reagents, fluorescent reagents and other light producing reagents.

11. The method of claim 8, wherein the nucleic acid primer is extended in the presence of at least one dideoxynucleotide.

12. The method of claim 11, wherein the dideoxynucleotide is dideoxyguanosine (ddG).

13. The method of claim 8, wherein the primer is extended in the presence of at least two dideoxynucleotides and the dideoxynucleotides are dideoxyguanosine (ddG) and dideoxycytosine (ddC).

14. A method for indicating a predisposition to cardiovascular disease in a subject, comprising:

the step of detecting in a target nucleic acid obtained from the subject the presence or absence of at least one allelic variant of polymorphic regions of a cytochrome C oxidase subunit VIb (COX6B) gene associated with high serum cholesterol or at least one allelic variant of polymorphic regions of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low serum HDL wherein the presence of an allelic variant is indicative of a predisposition to cardiovascular disease compared to a subject who does not comprise the allelic variant.

15. The method of claim 14, wherein the allelic variant is of a polymorphic region of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

16. The method of claim 15, wherein the polymorphic region is a single nucleotide polymorphism (SNP).

17. The method of claim 16, wherein the SNP is at position 2577 of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene sequence and the allelic variant is represented by an A nucleotide in the sense strand or a T nucleotide in the corresponding position in the antisense strand.

18. The method of claim 14, wherein the detecting step is by a method selected from the group consisting of allele specific hybridization, primer specific extension, oligonucleotide ligation assay, restriction enzyme site analysis and single-stranded conformation polymorphism analysis.

19. The method of claim 17, further comprising:

(a) hybridizing a target nucleic acid comprising a N-acetylglucosaminyl transferase component GPI-1 (GPI-1 )-encoding nucleic acid or fragment thereof with a nucleic acid primer that hybridizes adjacent to nucleotide 2577 of the GPI-1 gene;

(b) extending the nucleic acid primer using the target nucleic acid as a template; and

(c) determining the mass of the extended primer to identify the nucleotide present at position 2577, thereby determining the presence or absence of the allelic variant.

20. The method of claim 14, wherein the detecting step comprises mass spectrometry.

21. The method of claim 14, wherein the detecting step utilizes a signal moiety selected from the group consisting of:

radioisotopes, enzymes, antigens, antibodies, spectrophotometric reagents, chemiluminescent reagents, fluorescent reagents and other light producing reagents.

22. The method of claim 14, further comprising detecting the presence or absence of at least one allelic variant of polymorphic regions of another gene associated with cardiovascular disease, wherein the presence of the two allelic variants is associated with a predisposition to cardiovascular disease compared to a subject who does not comprise the combination of allelic variants.

23. The method of claim 22, wherein the other gene is selected from the group consisting of cholesterol ester transfer protein, plasma (CETP);

apolipoprotein A-IV (APO A4);

apolipoprotein A-I (APO A1);

apolipoprotein E (APO E);

apolipoprotein B (APO B);

apolipoprotein C-III (APO C3);

a gene encoding lipoprotein lipase (LPL);

ATP-binding cassette transporter (ABC

     1);

paraoxonase 1 (PON

     1);

paraoxonase 2 (PON

     2);

5,10-methylenetetrahydrofolate r reductase (MTHFR);

a gene encoding hepatic lipase, E-selectin, G protein beta 3 subunit and angiotensin II type 1 receptor gene.

24. The method of claim 22, wherein the two allelic variants are of the cytochrome C oxidase subunit VIb (COX6B) gene and the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

25. A method of screening for biologically active agents that modulate serum high density lipoprotein (HDL), comprising:

(a) combining a candidate agent with a cell comprising a nucleotide sequence encoding an allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low levels of serum HDL and operably linked to a promoter such that the nucleotide sequence is expressed as a GPI-1 protein in the cell; and

(b) determining the affect of the agent upon the expression and/or activity of the GPI-1 protein.

27. The method of claim 25, wherein the allelic variant is at position 2577 of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

26. A method of screening for biologically active agents that modulate serum high density lipoprotein (HDL), comprising:

(a) combining a candidate agent with a transgenic mouse comprising a transgenic nucleotide sequence stably integrated into the genome of the mouse encoding an allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low levels of serum HDL operably linked to a promoter, wherein the transgenic nucleotide sequence is expressed and the transgenic animal develops a low level of serum HDL; and

(b) determining the affect of the agent upon the serum HDL level.

28. The method of claim 26, wherein the allelic variant is at position 2577 of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

29. A method for predicting a response of a subject to a cardiovascular drug, comprising:

detecting the presence or absence of at least one allelic variant of a cytochrome C oxidase subunit VIb (COX6B) gene of the subject associated with high serum cholesterol or at least one allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene of the subject associated with low serum high density lipoprotein (HDL);

wherein the presence of at least one allelic variant is indicative of a positive response.

30. The method of claim 29, wherein the allelic variant is of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

31. A method for predicting a response of a subject to a biologically active agent that modulates serum high density lipoprotein (HDL), comprising:

detecting the presence or absence of at least one allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene of the subject associated with low HDL;

wherein the presence of an allelic variant is indicative of a positive response.

33. The method of claim 31, wherein the allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene is at position 2577.

32. A method for predicting a response of a subject to a biologically active agent that modulates serum high density lipoprotein (HDL) levels, comprising:

(a) detecting the presence or absence of at least one allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low HDL of the subject; and

(b) detecting the presence or absence of an allelic variant in at least one other gene of subject associated with cardiovascular disease, wherein the presence of both allelic variants is indicative of a positive response.

34. The method of claims 32, wherein the allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene is at position 2577.

35. The method of claim 32, wherein the other gene associated with cardiovascular disease is selected from the group of genes consisting of cytochrome C oxidase subunit VIb (COX6B);

cholesterol ester transfer protein, plasma (CETP);

apolipoprotein A-IV (APO A4);

apolipoprotein A-I (APO A1);

apolipoprotein E (APO E);

apolipoprotein B (APO B);

apolipoprotein C-III (APO C3);

a gene encoding lipoprotein lipase (LPL);

ATP-binding cassette transporter (ABC

     1);

paraoxonase 1 (PON

     1);

paraoxonase 2 (PON

     2);

5,10-methylenetetrahydrofolate r reductase (MTHFR);

a gene encoding hepatic lipase, E-selectin, G protein beta 3 subunit and angiotensin II type I receptor gene.

36. A primer or probe that specifically hybridizes adjacent to or at a polymorphic region of a cytochrome C oxidase subunit VIb (COX6B) gene associated with high serum cholesterol in combination with a primer or probe that specifically hybridizes adjacent to or at a polymorphic region of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low HDL.

37. The primers or probes of claim 36, further comprising primers or probes that specifically hybridizes adjacent to or at a polymorphic region of another gene associated with cardiovascular disease.

38. The primers or probes of claim 36, wherein the polymorphic region of the cytochrome C oxidase subunit VIb (COX6B) gene comprises nucleotide 86 of the coding strand and the polymorphic region of the N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene comprises nucleotide 2577.

39. The primers or probes of claim 37, wherein the other gene associated with cardiovascular disease is selected from the group of genes consisting of cholesterol ester transfer protein, plasma (CETP);

apolipoprotein A-IV (APO A4);

apolipoprotein A-I (APO A1);

apolipoprotein E (APO E);

apolipoprotein B (APO B);

apolipoprotein C-III (APO C3);

a gene encoding lipoprotein lipase (LPL);

ATP-binding cassette transporter (ABC

     1);

paraoxonase 1 (PON

     1);

paraoxonase 2 (PON

     2);

5,10-methylenetetrahydrofolate r reductase (MTHFR);

a gene encoding hepatic lipase, E-selectin, G protein beta 3 subunit and angiotensin II type 1 receptor gene.

40. A kit for indicating whether a subject has a predisposition to developing cardiovascular disease, comprising:

(a) at least one probe or primer that specifically hybridizes adjacent to or at a polymorphic region of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low serum high density lipoprotein (HDL).

41. The kit of claim 40 further comprising instructions for use.

42. The kit of claim 40, wherein the polymorphic region comprises nucleotide 2577 of the coding strand.

43. A kit for indicating whether a subject has a predisposition to developing cardiovascular disease, comprising:

(a) at least one probe or primer which specifically hybridizes adjacent to or at a polymorphic region of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene associated with low serum high density lipoprotein (HDL); and

(b) at least one probe or primer which specifically hybridizes adjacent to or at a polymorphic region of another gene associated with cardiovascular disease.

44. The kit of claim 43, further comprising instructions for use.

45. The kit of claim 43, wherein the other gene associated with cardiovascular disease is selected from the group of genes consisting of cytochrome C oxidase subunit VIb (COX6B);

cholesterol ester transfer protein, plasma (CETP);

apolipoprotein A-IV (APO A4);

apolipoprotein A-I (APO A1);

apolipoprotein E (APO E);

apolipoprotein B (APO B);

apolipoprotein C-III (APO C3);

a gene encoding lipoprotein lipase (LPL);

ATP-binding cassette transporter (ABC

     1);

paraoxonase 1 (PON

     1);

paraoxonase 2 (PON

     2);

5,10-methylenetetrahydrofolate r reductase (MTHFR);

a gene encoding hepatic lipase, E-selectin, G protein beta 3 subunit and angiotensin II type 1 receptor gene.

46. A method of diagnosing a predisposition to cardiovascular disease in a human, said method comprising the steps of:

(a) obtaining a biological sample from the human;

(b) isolating DNA from the biological sample; and

(c) detecting the presence or absence of at least one allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene in the DNA.

47. The method of claim 46, wherein at least one variant is a G to A transversion at position 2577 of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

49. The method of claim 46, wherein the detecting step is performed by an assay selected from the group consisting of allele specific hybridization, primer specific extension, oligonucleotide ligation, restriction enzyme site analysis, and single-stranded conformation polymorphism analysis.

48. A method of determining a response of a human to a cardiovascular drug, said method comprising the steps of:

(a) obtaining a biological sample from the human;

(b) isolating DNA from the biological sample; and

(c) detecting the presence or absence of at least one allelic variant of a cytochrome C oxidase subunit VIb (COX6B) gene in the DNA or at least one allelic variant of a N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene in the DNA.

50. The method of claim 48, wherein the detecting step is performed by an assay selected from the group consisting of allele specific hybridization, primer specific extension, oligonucleotide ligation, restriction enzyme site analysis, and single-stranded conformation polymorphism analysis.

51. A microarray comprising a nucleic acid having a sequence of a polymorphic region from a human N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

52. The microarray of claim 51, wherein the polymorphic region comprises a locus selected from the group consisting of position 2577 of the human N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene, position 2829 of the human GPI-1 gene, position 2519 of the human GPI-1 gene, position 2289 of the human GPI-1 gene, position 1938 of the human GPI-1 gene, position 1563 of the human GPI-1 gene, position 2656 of the human GPI-1 gene, and position 2664 of the human GPI-1 gene.

53. The microarray of claim 52, wherein the polymorphic region comprises position 2577 of the human N-acetylglucosaminyl transferase component GPI-1 (GPI-1) gene.

54. A kit comprising:

(a) at least one probe specific for a polymorphic region of a human gene selected from the group consisting of cytochrome C oxidase subunit VIb (COX6B);

N-acetylglucosaminyl transferase component GPI-1 (GPI-1);

cholesterol ester transfer protein, plasma (CETP);

apolipoprotein A-IV (APO A4);

apolipoprotein A-I (APO A1);

apolipoprotein E (APO E);

apolipoprotein B (APO B);

apolipoprotein C-III (APO C3);

a gene encoding lipoprotein lipase (LPL);

ATP-binding cassette transporter (ABC

     1);

paraoxonase 1 (PON

     1);

paraoxonase 2 (PON

     2);

5,10-methylenetetrahydrofolate r reductase (MTHFR);

a gene encoding hepatic lipase, E-selectin, G protein beta 3 subunit and angiotensin II type 1 receptor gene; and

(b) instructions for use.