Diagnostic polymorphisms of tgf-beta1 promoter

• US 20040170992A1
• Filed: 01/06/2004
• Published: 09/02/2004
• Est. Priority Date: 03/24/2000
• Status: Abandoned Application

• Current Assignee: Viral Therapeutics, Inc. (Vybion, Inc.)
• Original Assignee: Viral Therapeutics, Inc. (Vybion, Inc.)
• Inventors: Moskowitz, David W.
• Application Number:
  US10/467,149
• Publication Number:
  US 20040170992A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07K 14/495 Transforming growth factor [TGF]
• 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

Disclosed are single nucleotide polymorphisms (SNPs) associated with hypertension and end stage renal disease due to hypertension. Also disclosed are methods for using SNPs to determine susceptibility to end stage renal disease and hypertension; nucleotide sequences containing SNPs; kits for determining the presence of SNPs; and methods of treatment or prophylaxis based on the presence of SNPs.

Claims

1. A method for diagnosing a genetic susceptibility for a disease, condition, or disorder in a subject comprising:

obtaining a biological sample containing nucleic acid from said subject; and

analyzing said nucleic acid to detect the presence or absence of a single nucleotide polymorphism in the TGF-β

1 gene, wherein said single nucleotide polymorphism is associated with a genetic susceptibility for hypertension.

2. The method of claim 1, wherein the TGF-β

I gene comprises SEQ ID NO;

1.

3. The method of claim 1, wherein said nucleic acid is DNA, RNA, cDNA or mRNA.

4. The method of claim 2, wherein said single nucleotide polymorphism is located at position 474, 510, 546, or 563 of SEQ ID NO:

1.

5. The method of claim 4, wherein said single nucleotide polymorphism is a selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, C546->

T, G563->

A, and C563->

T.

6. The method of claim 1, wherein said analysis is accomplished by sequencing, mini sequencing, hybridization, restriction fragment analysis, oligonucleotide ligation assay or allele specific PCR.

7. An isolated polynucleotide comprising at least 10 contiguous nucleotides of SEQ ID NO:

1, or the complements thereof, and containing at least one single nucleotide polymorphism at position 474, 510, 546, or 563 of SEQ ID NO;

1 wherein said at least one single nucleotide polymorphism is associated with hypertension.

8. The isolated polynucleotide of claim 7, wherein at least one single nucleotide polymorphism is selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, C546->

T, G563->

A, and C563->

T.

9. The isolated polynucleotide of claim 7, wherein said at least one single nucleotide polymorphism is located at the 3′

end of said nucleic acid sequence.

10. The isolated polynucleotide of claim 7, further comprising a detectable label.

11. The isolated nucleic acid sequence of claim 10, wherein said detectable label is selected from the group consisting of radionuclides, fluorophores or fluorochromes, peptides, enzymes, antigens, antibodies, vitamins or steroids.

12. A kit comprising at least one isolated polynucleotide of at least 10 contiguous nucleotides of SEQ ID NO:

1 or the complement thereof, and containing at least one single nucleotide polymorphism associated with hypertension; and

instructions for using said polynucleotide for detecting the presence or absence of said at least one single nucleotide polymorphism in said nucleic acid.

13. The kit of claim 12 wherein said at least one single nucleotide polymorphism is located at position 474, 510, 546, or 563 of SEQ ID NO:

1.

14. The kit of claim 13 wherein said at least one single nucleotide polymorphism is selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, C546->

T, G563->

A, and C563->

T.

15. The kit of claim 12, wherein said single nucleotide polymorphism is located at the 3′

end of said polynucleotide.

16. The kit of claim 12, wherein said polynucleotide further comprises at least one detectable label.

17. The kit of claim 16, wherein said label is chosen from the group consisting of radionuclides, fluorophores or fluorochromes, peptides enzymes, antigens, antibodies, vitamins or steroids.

18. A kit comprising at least one polynucleotide of at least 10 contiguous nucleotides of SEQ ID NO:

1 or the complement thereof, wherein the 3′

end of said polynucleotide is immediately 5′

to a single nucleotide polymorphism site associated with hypertension; and

instructions for using said polynucleotide for detecting the presence or absence of said single nucleotide polymorphism in a biological sample containing nucleic acid.

19. The kit of claim 18, wherein said at least one polynucleotide further comprises a detectable label.

20. The kit of claim 19, wherein said detectable label is chosen from the group consisting of radionuclides, fluorophores or fluorochromes, peptides, enzymes, antigens, antibodies, vitamins or steroids.

21. A method for treatment or prophylaxis in a subject comprising:

obtaining a sample of biological material containing nucleic acid from a subject;

analyzing said nucleic acid to detect the presence or absence of at least one single nucleotide polymorphism in SEQ ID NO;

1 or the complement thereof associated with hypertension; and

treating said subject for said disease, condition or disorder.

22. The method of claim 21 wherein said nucleic acid is selected from the group consisting of DNA, cDNA, RNA and mRNA.

23. The method of claim 21, wherein said at least one single nucleotide polymorphism is located at position 474, 510, 546, or 563 of SEQ ID NO:

1.

24. The method of claim 21 wherein said at least one single nucleotide polymorphism is selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, C546->

T, G563->

A, and C563->

T.

25. The method of claim 21 wherein said treatment counteracts the effect of said at least one single nucleotide polymorphism detected.

26. A method for diagnosing a genetic susceptibility for a disease, condition, or disorder in a subject comprising:

obtaining a biological sample containing nucleic acid from said subject; and

analyzing said nucleic acid to detect the presence or absence of a single nucleotide polymorphism in the TGF-β

I gene, wherein said single nucleotide polymorphism is associated with a genetic susceptability for end stage renal disease due to hypertension.

27. The method of claim 26, wherein the TGF-PI gene comprises SEQ ID NO:

1.

28. The method of claim 26, wherein said nucleic acid is DNA, RNA, cDNA or mRNA.

29. The method of claim 27, wherein said single nucleotide polymorphism is located at position 474, 510, or 546 of SEQ ID NO:

1.

30. The method of claim 29, wherein said single nucleotide polymorphism is a selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, and C546->

T.

31. The method of claim 26, wherein said analysis is accomplished by sequencing, mini sequencing, hybridization, restriction fragment analysis, oligonucleotide ligation assay or allele specific PCR.

32. An isolated polynucleotide comprising at least 10 contiguous nucleotides of SEQ ID NO:

1, or the complements thereof, and containing at least one single nucleotide polymorphism at position 474, 510, or 546 of SEQ ID NO;

1 wherein said at least one single nucleotide polymorphism is associated with end stage renal disease due to hypertension.

33. The isolated polynucleotide of claim 32, wherein at least one single nucleotide polymorphism is selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, and C546->

T.

34. The isolated polynucleotide of claim 32, wherein said at least one single nucleotide polymorphism is located at the 3′

end of said nucleic acid sequence.

35. The isolated polynucleotide of claim 32, further comprising a detectable label.

36. The isolated nucleic acid sequence of claim 34, wherein said detectable label is selected from the group consisting of radionuclides, fluorophores or fluorochromes, peptides, enzymes, antigens, antibodies, vitamins or steroids.

37. A kit comprising at least one isolated polynucleotide of at least 10 contiguous nucleotides of SEQ ID NO:

1 or the complement thereof, and containing at least one single nucleotide polymorphism associated with end stage renal disease due to hypertension; and

instructions for using said polynucleotide for detecting the presence or absence of said at least one single nucleotide polymorphism in said nucleic acid.

38. The kit of claim 37 wherein said at least one single nucleotide polymorphism is located at position 474, 510, or 546 of SEQ ID NO:

1.

39. The kit of claim 38 wherein said at least one single nucleotide polymorphism is selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, and C546->

T.

40. The kit of claim 37, wherein said single nucleotide polymorphism is located at the 3′

end of said polynucleotide.

41. The kit of claim 37, wherein said polynucleotide further comprises at least one detectable label.

42. The kit of claim 41, wherein said label is chosen from the group consisting of radionuclides, fluorophores or fluorochromes, peptides enzymes, antigens, antibodies, vitamins or steroids.

43. A kit comprising at least one polynucleotide of at least 10 contiguous nucleotides of SEQ ID NO:

1 or the complement thereof, wherein the 3′

end of said polynucleotide is immediately 5′

to a single nucleotide polymorphism site associated with end stage renal disease due to hypertension; and

instructions for using said polynucleotide for detecting the presence or absence of said single nucleotide polymorphism in a biological sample containing nucleic acid.

44. The kit of claim 43, wherein said at least one polynucleotide further comprises a detectable label.

45. The kit of claim 44, wherein said detectable label is chosen from the group consisting of radionuclides, fluorophores or fluorochromes, peptides, enzymes, antigens, antibodies, vitamins or steroids.

46. A method for treatment or prophylaxis in a subject comprising:

obtaining a sample of biological material containing nucleic acid from a subject;

analyzing said nucleic acid to detect the presence or absence of at least one single nucleotide polymorphism in SEQ ID NO;

1 or the complement thereof associated with end stage renal disease due to hypertension; and

treating said subject for said disease, condition or disorder.

47. The method of claim 46 wherein said nucleic acid is selected from the group consisting of DNA, cDNA, RNA and mRNA.

48. The method of claim 46, wherein said at least one single nucleotide polymorphism is located at position 474, 510, or 546 of SEQ ID NO:

1.

49. The method of claim 46 wherein said at least one single nucleotide polymorphism is selected from the group consisting of G474->

T, C474->

A, C510->

G, G510->

C, G546->

A, and C546->

T.

50. The method of claim 46 wherein said treatment counteracts the effect of said at least one single nucleotide polymorphism detected.