Methods for diagnosing osteoporosis or a susceptibility to osteoporosis based on haplotype association

• US 20060057612A1
• Filed: 07/18/2005
• Published: 03/16/2006
• Est. Priority Date: 09/14/2000
• Status: Abandoned Application

• Current Assignee: Decode Genetics Ehf. (Amgen Inc.)
• Original Assignee: Decode Genetics Ehf. (Amgen Inc.)
• Inventors: Gulcher, Jeffrey R., Styrkarsdottir, Unnur, Cazier, Jean-Baptiste
• Application Number:
  US11/185,033
• Publication Number:
  US 20060057612A1
• 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

Methods for diagnosis of osteoporosis or a susceptibility to osteoporosis based on detection of at risk haplotypes associated with BMP2 are disclosed.

Claims

1. A method of diagnosing osteoporosis or a susceptibility to osteoporosis in an individual, comprising detecting the presence or absence of at least one at-risk haplotype comprising a haplotype selected from the group consisting of:

haplotype I, haplotype II, haplotype a, haplotype b, haplotype c, haplotype d and combinations thereof, wherein the presence of the haplotype is indicative of osteoporosis or a susceptibility to osteoporosis;

2. A method for assaying the presence of a first nucleic acid molecule in a sample, comprising contacting said sample with a second nucleic acid molecule comprising the haplotype of claim 1.

3. The method of claim 1, wherein determining the presence or absence of the haplotype comprises 1) enzymatic amplification of nucleic acid from the individual, 2) enzymatic amplification and electrophoretic analysis, 3) restriction fragment length polymorphism analysis, or 4) sequence analysis.

4-20. -20. (canceled)

21. A reagent kit for assaying a sample for the presence of at least one haplotype associated with osteoporosis, wherein the haplotype comprises two or more specific alleles, comprising in separate containers:

a) one or more labeled nucleic acids capable of detecting one or more specific alleles of the haplotype; and

b) reagents for detection of said label.

22. The reagent kit of claim 21, wherein the labeled nucleic acid comprises at least one contiguous nucleotide sequence that is completely complementary to a region comprising at least one specific allele of the haplotype.

23. (canceled)

24. A method for the diagnosis and identification of susceptibility to osteoporosis in an individual, comprising:

screening for at least one at-risk haplotype associated with BMP2 that is more frequently present in an individual susceptible to osteoporosis compared to an individual who is not susceptible to osteoporosis wherein the at-risk haplotype increases the risk significantly.

25. The method of claim 24, wherein the significant increase is at least about 20%.

26. The method of claim 25, wherein the significant increase is identified as an odds ratio of at least about 1.2.

27-31. -31. (canceled)

32. A method for diagnosing a susceptibility to osteoporosis in an individual, comprising:

obtaining a nucleic acid sample from the individual; and

analyzing the nucleic acid sample for the presence or absence of at least one haplotype comprising two or more alleles selected from the group consisting of;

TSC0898956, B420, B8463, D20S846, TSC0191642, P4337, D20S892, B5048, B9082, D20S59, B7111/rs235764 B12845/rs15705, P9313, B10631, D35548, rs1116867, TSC0278787, D35548 and TSC0271643, wherein the presence of the haplotype is indicative of susceptibility to osteoporosis.

33. The method of claim 32, wherein the haplotype comprises a) two or more alleles selected from the group consisting of:

TSC0898956, B420, B8463, D20S846 and TSC0191642, b) two or more alleles selected from the group consisting of;

P4337, D20S892, B5048, B9082 and D20S59, c) B7111/rs235764 or B12845/rs15705, d) two or more alleles selected from the group consisting of;

P9313, B10631 and D35548, e) two or more alleles selected from the group consisting of;

rs1116867, TSC0278787 and D35548, or f) two or more alleles selected from the group consisting of;

TSC0271643, P9313 and B7111.

34-38. -38. (canceled)

39. A method of diagnosing osteoporosis or a susceptibility to osteoporosis in an individual, comprising detecting the presence or absence of at least one at-risk haplotype comprising a haplotype selected from the group consisting of:

haplotype G, haplotype V, and combinations thereof, wherein the presence of the haplotype is indicative of osteoporosis or a susceptibility to osteoporosis.

40. A method for assaying the presence of a first nucleic acid molecule in a sample, comprising contacting said sample with a second nucleic acid molecule comprising the haplotype of claim 39.

41. The method of claim 39, wherein determining the presence or absence of the haplotype comprises 1) enzymatic amplification of nucleic acid from the individual, 2) enzymatic amplification and electrophoretic analysis, 3) restriction fragment length polymorphism analysis or, 4) sequence analysis.

45. A kit for assaying a sample for the presence of at least one haplotype associated with osteoporosis of claim 39, wherein the haplotype comprises one or more specific alleles, and wherein the kit comprises one or more nucleic acids capable of detecting the presence or absence of one or more of the specific alleles, thereby indicating the presence or absence of the haplotype in the sample.

46. The kit of claim 45, wherein the nucleic acid comprises at least one contiguous nucleotide sequence that is completely complementary to a region comprising at least one specific allele of the haplotype.

42-44. -44. (canceled)

47-54. -54. (canceled)

55. A method for diagnosing a susceptibility to osteoporosis in an individual, comprising:

obtaining a nucleic acid sample from the individual; and

analyzing the nucleic acid sample for the presence or absence of a haplotype comprising one or more alleles selected from the group consisting of;

SG20S405, SG20S407, SG20S381, SG20S171, SG20S174, SG20S195 and D20S846, wherein the presence of the haplotype is indicative of susceptibility to osteoporosis.

56. The method of claim 55, wherein the haplotype comprises one or more alleles selected from the group consisting of:

SG20S405, SG20S407 and SG20S381.

57. The method of claim 55, wherein the haplotype comprises one or more alleles selected from the group consisting of:

SG20S174, SG20S195 and D20S846.

58. A method of diagnosing a susceptibility to osteoporosis in an individual, comprising detecting at least one polymorphism in a human BMP2 gene of SEQ ID NO:

1, wherein the polymorphism is selected from the group consisting of those listed in FIGS. 9.1 through 9.227.

59. The method of claim 58, wherein the polymorphism is detected in a sample from a source selected from the group consisting of:

blood, serum, cells and tissue.

60. An isolated nucleic acid molecule comprising the nucleic acid of SEQ ID NO:

1 with one or more of the nucleic acid changes selected from the group consisting of those listed in FIGS. 12.1 through 12.13 and 13.