Diagnostic polymorphisms for the tgf-beta1 promoter

• US 20040209254A1
• Filed: 08/05/2003
• Published: 10/21/2004
• Est. Priority Date: 07/25/2000
• Status: Abandoned Application

• Current Assignee: Viral Therapeutics, Inc. (Vybion, Inc.)
• Original Assignee: Viral Therapeutics, Inc. (Vybion, Inc.)
• Inventors: Henderson, Lee A.
• Application Number:
  US10/333,892
• Publication Number:
  US 20040209254A1
• 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 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Disclosed are single nucleotide polymorphisms (SNPs) associated with breast cancer, prostate cancer stage D, colon cancer, lung cancer, hypertension, atherosclerotic peripheral vascular disease due to hypertension, cerebrovascular accident due to hypertension, cataracts due to hypertension, hypertensive cardiomyopathy, myocardial infarction due to hypertension, end stage renal disease due to hypertension, non-insulin dependent diabetes mellitus, atherosclerotic peripheral vascular disease due to non-insulin dependent diabetes mellitus, cerebrovascular accident due to non-insulin dependent diabetes mellitus, ischemic cardiomyopathy, ischemic cardiomyopathy with non-insulin dependent diabetes mellitus, myocardial infarction due to non-insulin dependent diabetes mellitus, atrial fibrillation without valvular disease, alcohol abuse, anxiety, asthma, chronic obstructive pulmonary disease, cholecysteclomy degenerative joint disease, end stage renal disease and frequent de-clots, end stage renal disease due to focal segmental glomerular sclerosis, end stage renal disease due to insulin dependent diabetes mellitus, and seizure disorder. Also disclosed are methods for using the SNPs to determine susceptibility to these diseases; nucleotide sequences containing the SNPs; kits for determining the presence of the SNPs; and methods of treatment or prophylaxis based on the presence of the 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 predisposition for a disease, condition or disorder selected from the group consisting of breast cancer, prostate cancer stage D, colon cancer, lung cancer, hypertension, atherosclerotic peripheral vascular disease due to hypertension, cerebrovascular accident due to hypertension, cataracts due to hypertension, hypertensive cardiomyopathy, myocardial infarction due to hypertension, end stage renal disease due to hypertension, non-insulin dependent diabetes mellitus, atherosclerotic peripheral vascular disease due to non-insulin dependent diabetes mellitus, cerebrovascular accident due to non-insulin dependent diabetes mellitus, ischemic cardiomyopathy, ischemic cardiomyopathy with non-insulin dependent diabetes mellitus, myocardial infarction due to non-insulin dependent diabetes mellitus, atrial fibrillation without valvular disease, alcohol abuse, anxiety, asthma, chronic obstructive pulmonary disease, cholecystectomy, degenerative joint disease, end stage renal disease and frequent de-clots, end stage renal disease due to focal segmental glomerular sclerosis, end stage renal disease due to insulin dependent diabetes mellitus, and seizure disorder.

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

1 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 216 or 563 of SEQ ID NO:

1.

5. The method of claim 4, wherein said single nucleotide polymorphism is selected from the group consisting of C216->

G and G563->

A and the complements thereof namely G216->

C 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 complement thereof, and containing at least one single nucleotide polymorphism at position 216 or 563 of SEQ ID NO;

1 wherein said at least one single nucleotide polymorphism is associated with a disease, condition or disorder selected from the group consisting of breast cancer, prostate cancer stage D, colon cancer, lung cancer, hypertension, atherosclerotic peripheral vascular disease due to hypertension, cerebrovascular accident due to hypertension, cataracts due to hypertension, hypertensive cardiomyopathy, myocardial infarction due to hypertension, end stage renal disease due to hypertension, non-insulin dependent diabetes mellitus, atherosclerotic peripheral vascular disease due to non-insulin dependent diabetes mellitus, cerebrovascular accident due to non-insulin dependent diabetes mellitus, ischemic cardiomyopathy, ischemic cardiomyopathy with non-insulin dependent diabetes mellitus, myocardial infarction due to non-insulin dependent diabetes mellitus, atrial fibrillation without valvular disease, alcohol abuse, anxiety, asthma, chronic obstructive pulmonary disease, cholecystectomy, degenerative joint disease, end stage renal disease and frequent de-clots, end stage renal disease due to focal segmental glomerular sclerosis, end stage renal disease due to insulin dependent diabetes mellitus, and seizure disorder.

8. The isolated polynucleotide of claim 7, wherein at least one single nucleotide polymorphism is selected from the group consisting of C216->

G and G563->

A and the complements thereof namely G216->

C 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 a disease, condition, or disorder selected from the group consisting of breast cancer, prostate cancer stage D, colon cancer, lung cancer, hypertension, atherosclerotic peripheral vascular disease due to hypertension, cerebrovascular accident due to hypertension, cataracts due to hypertension, hypertensive cardiomyopathy, myocardial infarction due to hypertension, end stage renal disease due to hypertension, non-insulin dependent diabetes mellitus, atherosclerotic peripheral vascular disease due to non-insulin dependent diabetes mellitus, cerebrovascular accident due to non-insulin dependent diabetes mellitus, ischemic cardiomyopathy, ischemic cardiomyopathy with non-insulin dependent diabetes mellitus, myocardial infarction due to non-insulin dependent diabetes mellitus, atrial fibrillation without valvular disease, alcohol abuse, anxiety, asthma, chronic obstructive pulmonary disease, cholecystectomy, degenerative joint disease, end stage renal disease and frequent de-clots, end stage renal disease due to focal segmental glomerular sclerosis, end stage renal disease due to insulin dependent diabetes mellitus, and seizure disorder; 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 216 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 C216->

G and G563->

A and the complements thereof namely G216->

C 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 a genetic predisposition to disease, condition, or disorder selected from the group consisting of breast cancer, prostate cancer stage D, colon cancer, lung cancer, hypertension, atherosclerotic peripheral vascular disease due to hypertension, cerebrovascular accident due to hypertension, cataracts due to hypertension, hypertensive cardiomyopathy, myocardial infarction due to hypertension, end stage renal disease due to hypertension, non-insulin dependent diabetes mellitus, atherosclerotic peripheral vascular disease due to non-insulin dependent diabetes mellitus, cerebrovascular accident due to non-insulin dependent diabetes mellitus, ischemic cardiomyopathy, ischemic cardiomyopathy with non-insulin dependent diabetes mellitus, myocardial infarction due to non-insulin dependent diabetes mellitus, atrial fibrillation without valvular disease, alcohol abuse, anxiety, asthma, chronic obstructive pulmonary disease, cholecystectorny, degenerative joint disease, end stage renal disease and frequent de-clots, end stage renal disease due to focal segmental glomerular sclerosis, end stage renal disease due to insulin dependent diabetes mellitus, and seizure disorder; 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 single nucleotide polymorphism site is located at position 216 or 563 of SEQ ID NO:

1.

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

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

22. 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 a disease, condition, or disorder selected from the group consisting of breast cancer, prostate cancer stage D, colon cancer, lung cancer, hypertension, atherosclerotic peripheral vascular disease due to hypertension, cerebrovascular accident due to hypertension, cataracts due to hypertension, hypertensive cardiomyopathy, myocardial infarction due to hypertension, end stage renal disease due to hypertension, non-insulin dependent diabetes mellitus, atherosclerotic peripheral vascular disease due to non-insulin dependent diabetes mellitus, cerebrovascular accident due to non-insulin dependent diabetes mellitus, ischemic cardiomyopathy, ischemic cardiomyopathy with non-insulin dependent diabetes mellitus, myocardial infarction due to non-insulin dependent diabetes mellitus, atrial fibrillation without valvular disease, alcohol abuse, anxiety, asthma, chronic obstructive pulmonary disease, cholecystectomy, degenerative joint disease, end stage renal disease and frequent de-clots, end stage renal disease due to focal segmental glomerular sclerosis, end stage renal disease due to insulin dependent diabetes mellitus, and seizure disorder; and

treating said subject for said disease, condition or disorder.

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

24. The method of claim 22, wherein said at least one single nucleotide polymorphism is located at position 216 or 563 of SEQ ID NO:

1.

25. The method of claim 22 wherein said at least one single nucleotide polymorphism is selected from the group of C216->

G and G563->

A and the complements thereof namely G216->

C and C563->

T.

26. The method of claim 22 wherein said treatment counteracts the effect of said at least one single nucleotide polymorphism detected.