Single nucleotide polymorphisms diagnostic for schizophrenia

• US 20030224365A1
• Filed: 04/19/2002
• Published: 12/04/2003
• Est. Priority Date: 04/24/2001
• Status: Abandoned Application

• Current Assignee: Chi-Hse Teng, Kathleen A. Schellin, Linda Susan Wood
• Original Assignee: Chi-Hse Teng, Kathleen A. Schellin, Linda Susan Wood
• Inventors: Schellin, Kathleen A., Wood, Linda Susan, Teng, Chi-Hse
• Application Number:
  US10/126,063
• Publication Number:
  US 20030224365A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61P 25/18 Antipsychotics, i.e. neuroleptics; Drugs for mania or schizophrenia
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

The invention provides nucleic acid segments of the human G protein coupled receptor Con-202 gene including polymorphic sites. Allele specific primers and probes hybridizing to regions flanking these sites are also provided. The invention also provides methods for determining the genetic risk of developing schizophrenia or diagnosing schizophrenia.

Claims

1. An isolated polynucleotide consisting of between 12 and 200 contiguous nucleotides of SEQ ID NO 1 or its complement including at least one Con-202 polymorphic site selected from the group consisting of the polymorphic sites at positions 184, 1022, 1292, 1400, 2296, 2369 and 2724.

2. The isolated polynucleotide of claim 1 in which the nucleotide at position 184 is selected from the group of nucleotides G or C

3. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 2.

4. The isolated polynucleotide of claim 1 in which the nucleotide at position 1022 is selected from the group of nucleotides C or A

5. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 4.

6. The isolated polynucleotide of claim 1 in which the nucleotide at position 1292 is selected from the group of nucleotides C or T.

7. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 6.

8. The isolated polynucleotide of claim 1 in which the nucleotide at position 1400 is selected from the group of nucleotides C or T.

9. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 8.

10. The isolated polynucleotide of claim 1 in which the nucleotide at position 2296 is selected from the group of nucleotides T or A.

11. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 10.

12. The isolated polynucleotide of claim 1 in which the nucleotide at position 2369 is selected from the group of nucleotides G or A.

13. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 12.

14. The isolated polynucleotide of claim 1 in which the nucleotide at position 2724 is selected from the group of nucleotides A or G.

15. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 14.

16. The isolated polynucleotide of claim 1 that is less than 200 nucleotides

17. The isolated polynucleotide of claim 1 that is less than 50 nucleotides.

18. The isolated polynucleotide of claim 1 that is less than 20 nucleotides.

19. The isolated polynucleotide of claim 1 wherein the polymorphism is within 4 nucleotides of the center of said polynucleotide.

20. The isolated polynucleotide of claim 1 wherein the polymorphism is at the center of said polynucleotide.

21. The isolated polynucleotide of claim 1 wherein the polymorphism is at the end of said polynucleotide.

22. The isolated polynucleotide of claim 1 wherein the polynucleotide is a probe.

23. The isolated polynucleotide of claim 1 wherein the polynucleotide is a primer.

24. An isolated polynucleotide comprising at least 12 contiguous nucleotides of SEQ ID NO:

1 or its complement including at least one Con-202 polymorphic site selected from the group consisting of the Con-202 polymorphic sites at positions 184, 1022, 2296 and 2369 wherein said Con-202 polymorphic site or sites is occupied by at least one rare allele selected from the group consisting of C at position 184, A at position 1022, A at position 2296 and A at position 2369.

25. An isolated polynucleotide according to claim 24 comprising at least 12 contiguous nucleotides of SEQ ID NO:

1 including the nucleotide at position 184 wherein position 184 is occupied by a C.

26. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 25.

27. An isolated polynucleotide according to claim 24 comprising at least 12 contiguous nucleotides of SEQ ID NO:

1 including the nucleotide at position 1022 wherein position 1022 is occupied by an A.

28. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 27.

29. An isolated polynucleotide according to claim 24 comprising at least 12 contiguous nucleotides of SEQ ID NO:

1 including the nucleotide at position 2296 wherein position 2296 is occupied by an A.

30. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 29.

31. An isolated polynucleotide according to claim 24 comprising at least 12 contiguous nucleotides of SEQ ID NO:

1 including the nucleotide at position 2369 wherein position 2369 is occupied by an A.

32. The isolated polynucleotide which is the complement of the isolated polynucleotide of claim 31.

58. The method of claim 30 wherein the determining comprises double PCR amplification of specific alleles.

33. A method for classifying a nucleic acid molecule encoding Con-202 or a fragment thereof from an individual comprising

(a) obtaining said nucleic acid from said individual;

and

(b) determining a nucleotide from said nucleic acid which corresponds to the nucleotide occupying at least one polymorphic site selected from the group consisting of the polymorphic sites at positions 184, 1022, 1292, 1400, 2296, 2369 and 2724

34. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a G

35. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a C

36. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 1022 of SEQ ID NO:

1 or a fragment thereof is a C

37. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 1022 of SEQ ID NO:

1 or a fragment thereof is an A.

38. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 1292 of SEQ ID NO:

1 or a fragment thereof is a C.

39. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 1292 of SEQ ID NO:

1 or a fragment thereof is a T.

40. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 1400 of SEQ ID NO:

1 or a fragment thereof is a C

41. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 1400 of SEQ ID NO:

1 or a fragment thereof is a T

42. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 2724 of SEQ ID NO:

1 or a fragment thereof is an A

43. The method of claim 33, wherein the determining comprises determining whether the nucleotide occupying position 2724 of SEQ ID NO:

1 or a fragment thereof is a G

44. The method of claim 33, wherein the determining comprises amplification of the DNA.

60. The method of claim 43 wherein the presence of a G at position 184 indicates that the individual is more likely to suffer from schizophrenia.

61. The method of claim 43 wherein the presence of a C at position 184 indicates that the individual is less likely to suffer from schizophrenia.

62. The method of claim 43 wherein the presence of an A at position 2724 indicates that the individual is more likely to suffer from schizophrenia.

63. The method of claim 43 wherein the presence of an G at position 2724 indicates that the individual is less likely to suffer from schizophrenia.

77. A method of determining the frequency in a population of an Con-202 polymorphism, comprising:

a) genotyping individuals from said population for said polymorphism according to the method of claim 33;

and

b) determining the proportional representation of said polymorphism in said population.

78. The method of detecting an association between a Con-202 polymorphism and a phenotype, comprising the steps of:

a) determining the frequency of at least one Con-202 polymorphism in a trait positive population according to the method of claim 77;

b) determining the frequency of said Con-202 polymorphism in a control population according to the method of claim 77;

and

c) determining whether a statistically significant association exists between said polymorphism and said phenotype.

79. The method according to claim 78 wherein said phenotype is response to an agent acting on schizophrenia

80. The method according to claim 78 wherein said phenotype is a side effect to an agent acting on schizophrenia

81. A method of estimating the frequency of a haplotype for a set of polymorphic markers in a population, comprising:

a) genotyping each individual in said population for at least one Con-202 polymorphism according to claim 33;

b) genotyping each individual in said population for a second polymorphic marker by determining the identity of the nucleotides at said second polymorphic marker for both copies of said second polymorphic marker present in the genome; and

c) applying a haplotype determination method to the identities of the nucleotides determined in steps a) and b) to obtain an estimate of said frequency.

82. The method according to claim 81, wherein said haplotype determination method is selected from the group consisting of asymmetric PCR amplification, double PCR amplification of specific alleles, the Clark method, the Clayton method, or an expectation maximization algorithm.

45. A method of haplotype determination in an individual for diagnostic or prognostic purposes, comprising

obtaining said nucleic acid from said individual;

and

determining the nucleotides from said nucleic acid which correspond to the nucleotides occupying more than one Con-202 polymorphic site selected from the group consisting of the Con-202 polymorphic sites at positions;

(a) 184 and 1292,

(b) 184 and 1400,

(c) 184 and 1022,

(c) 184 and 2724 and

(d) 184 and 1022 and 2724

on a single chromosome.

46. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 and 1292 of SEQ ID NO:

1 or a fragment thereof are both C.

47. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a C and whether the nucleotide occupying position 1292 of SEQ ID NO;

1 or a fragment thereof is a T.

48. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 and 1400 of SEQ ID NO:

1 or a fragment thereof are both C.

49. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a C and whether the nucleotide occupying position 1400 of SEQ ID NO;

1 or a fragment thereof is a T.

50. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 and 1022 of SEQ ID NO:

1 or a fragment thereof are both C.

51. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a G and whether the nucleotide occupying position 1022 of SEQ ID NO;

1 or a fragment thereof is a C.

52. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a G and whether the nucleotide occupying position 1022 of SEQ ID NO;

1 or a fragment thereof is a A.

53. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a C and whether the nucleotide occupying position 2724 of SEQ ID NO;

1 or a fragment thereof is a G.

54. The method of claim 45, wherein the determining comprises determining whether the nucleotide occupying position 184 of SEQ ID NO:

1 or a fragment thereof is a G and whether the nucleotide occupying position 2724 of SEQ ID NO;

1 or a fragment thereof is a A.

55. The method of claim 45, wherein the determining comprises:

determining whether the nucleotide occupying position 184 of SEQ ID NO;

1 or a fragment thereof is a C,

determining whether the nucleotide occupying position 1022 of SEQ ID NO;

1 or a fragment thereof is a C and

determining whether the nucleotide occupying position 2724 of SEQ ID NO;

1 or a fragment thereof is a G.

56. The method of claim 45, wherein the determining comprises:

determining whether the nucleotide occupying position 184 of SEQ ID NO;

1 or a fragment thereof is a G,

determining whether the nucleotide occupying position 1022 of SEQ ID NO;

1 or a fragment thereof is a C and

determining whether the nucleotide occupying position 2724 of SEQ ID NO;

1 or a fragment thereof is an A.

57. The method of claim 45, wherein the determining comprises amplification of the DNA

59. A method of predicting a whether an individual is more or less likely to suffer from schizophrenia comprising:

determining the nucleotide from a nucleic acid sample from said patient which corresponds to the nucleotide occupying a Con-202 polymorphic site selected from the group consisting of the Con-202 polymorphic sites at positions;

184 and 2724.

64. A method of predicting a whether an individual is more or less likely to suffer from schizophrenia comprising:

determining the nucleotides from a nucleic acid sample from said patient which correspond to two or more nucleotides occupying two or more Con-202 polymorphic sites on a single chromosome selected from the group consisting of the Con-202 polymorphic sites at positions;

(a) 184 and 1292,

(b) 184 and 1400,

(c) 184 and 1022,

(c) 184 and 2724 and

(d) 184 and 1022 and 2724

65. The method of claim 64 wherein a C at both positions 184 and 1292 indicates that the individual is less likely to suffer from schizophrenia.

66. The method of claim 64 wherein a C at position 184 and a T at position 1292 indicates that the individual is less likely to suffer from schizophrenia.

67. The method of claim 66 wherein a C at both positions 184 and 1400 indicates that the individual is less likely to suffer from schizophrenia.

68. The method of claim 66 wherein a C at position 184 and a T at position 1400 indicates that the individual is less likely to suffer from schizophrenia.

69. The method of claim 66 wherein a G at position 184 and a C at position 1022 indicates that the individual is more likely to suffer from schizophrenia.

70. The method of claim 66 wherein a C at both positions 184 and 1022 indicates that the individual is less likely to suffer from schizophrenia.

71. The method of claim 66 wherein a G at position 184 and an A at position 1022 indicates that the individual is less likely to suffer from schizophrenia.

72. The method of claim 66 wherein a G at position 184 and an A at position 2724 indicates that the individual is more likely to suffer from schizophrenia.

73. The method of claim 66 wherein a G at both positions 184 and 2724 indicates that the individual is less likely to suffer from schizophrenia.

74. The method of claim 66 wherein a C at position 184 and an G at position 2724 indicates that the individual is less likely suffer from schizophrenia.

75. The method of claim 66 wherein a C at both positions 184 and 1022 and a G at position 2724 indicates that the individual is more likely to suffer from schizophrenia.

76. The method of claim 66 wherein a G at position 184, a C at position 1022, and an A at position 2724 indicates that the individual is less likely to suffer from schizophrenia.

83. A diagnostic kit comprising the required components for the determination of the of the identity of the nucleotide occupying a Con-202 polymorphic site in small volumes in a self contained kit.

84. The diagnostic kit of claim 83 comprising an isolated polynucleotide comprising between 12 and 200 contiguous nucleotides of SEQ ID NO 1 or its complement including at least one polymorphic site.