Claims
- 1. A method of assessing sensitivity to a therapeutic agent in a subject with a chronic obstructive pulmonary disease (COPD) or asthma, comprising:
determining a genotype of the subject, wherein the genotype of the subject is defined by a nucleotide sequence of a region of at least one gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD11B1, HSD11B2, MAPK8, NFATC4, SCYA11 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-β, and wherein the presence of a sequence variation in the region of the at least one gene is indicative of sensitivity to the therapeutic agent.
- 2. The method of claim 1, wherein the genotype of the subject is defined by a nucleotide sequence of a region of CRHR1.
- 3. The method of claim 1, wherein the sequence variation is a single nucleotide polymorphism.
- 4. The method of claim 3, wherein the single nucleotide polymorphism is in a nucleotide sequence found in a region of CRHR1, wherein the nucleotide sequence comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 5. The method of claim 1, wherein the sequence variation is selected from the group consisting of a deletion and insertion.
- 6. The method of claim 1, wherein the sequence variation indicates a haplotype.
- 7. The method of claim 6, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 8. The method of claim 7, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs1876828 or rs242939.
- 9. The method of claim 7, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs242939 and rs242941.
- 10. The method of claim 7, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs1876828 and rs242941.
- 11. The method of claim 7, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 and rs242941.
- 12. The method of claim 11, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 and rs242941, and wherein the haplotype is the GAT haplotype.
- 13. The method of claim 12, wherein the subject is homozygous for the GAT haplotype.
- 14. The method of claim 1, wherein the sequence variation is determined with a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.
- 15. The method of claim 14, wherein the nucleic acid hybridization is performed using a nucleic acid probe.
- 16. The method of claim 14, wherein the nucleic acid hybridization is performed using a nucleic acid microarray.
- 17. The method of claim 14, wherein the nucleic acid amplification is performed using PCR.
- 18. The method of claim 1, wherein the therapeutic agent is an inhaled corticosteroid.
- 19. The method of claim 1, wherein the therapeutic agent is a bronchodilator (beta-agonist).
- 20. The method of claim 1, wherein the COPD is selected from the group consisting of chronic bronchitis, emphysema, bronchioectasis and extrinsic allergic alveolitis.
- 21. The method of claim 1, wherein the subject has asthma.
- 22. The method of claim 1, wherein the presence of the sequence variation is indicative that the subject is not sensitive to the therapeutic agent.
- 23. The method of claim 1, further comprising assessing at least one risk factor to assess the sensitivity to the therapeutic agent.
- 24. The method of claim 12, wherein the risk factor is selected from the group consisting of baseline level of lung function, gender, age, race and prior steroid use.
- 25. A method of assessing sensitivity to a corticosteroid or beta-agonist in a subject, comprising:
determining a genotype of the subject, wherein the genotype of the subject is defined by a nucleotide sequence of a region of at least one gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD11B1, HSD11B2, MAPK8, NFATC4, SCYA1 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-β, and wherein the presence of a sequence variation in the region of the at least one gene is indicative of sensitivity to the corticosteroid or beta-agonist.
- 26. The method of claim 25, wherein the subject has COPD or asthma.
- 27. The method of claim 25, wherein the subject suffers from depression.
- 28. The method of claim 25, wherein the genotype of the subject is defined by a nucleotide sequence of a region of CRHR1.
- 29. The method of claim 25, wherein the sequence variation is a single nucleotide polymorphism.
- 30. The method of claim 29, wherein the single nucleotide polymorphism is in a nucleotide sequence found in a region of CRHR1, wherein the nucleotide sequence comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 31. The method of claim 25, wherein the sequence variation is selected from the group consisting of a deletion and insertion.
- 32. The method of claim 25, wherein the sequence variation indicates a haplotype.
- 33. The method of claim 32, wherein the haplotype is defined by a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 34. The method of claim 25, wherein the sequence variation is determined with a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.
- 35. The method of claim 34, wherein the nucleic acid hybridization is performed using a nucleic acid probe.
- 36. The method of claim 34, wherein the nucleic acid hybridization is performed using a nucleic acid microarray.
- 37. The method of claim 34, wherein the nucleic acid amplification is performed using PCR.
- 38. A method of assessing sensitivity to a therapeutic agent in a subject with a chronic obstructive pulmonary disease (COPD) or asthma, comprising:
determining a genotype of the subject, wherein the genotype of the subject is defined by a nucleotide sequence of a region of NR3C1, and wherein the presence of a sequence variation in the region of NR3C1 is indicative of sensitivity to the therapeutic agent.
- 39. The method of claim 38, wherein the nucleotide sequence is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 89-121 and 309-324.
- 39. The method of claim 38, wherein the nucleotide sequence is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 89 and 100.
- 40. The method of claim 38, wherein the sequence variation is a single nucleotide polymorphism.
- 41. The method of claim 38, wherein the sequence variation is selected from the group consisting of a deletion and insertion.
- 41. The method of claim 38, wherein the sequence variation indicates a haplotype.
- 43. The method of claim 38, wherein the sequence variation is determined with a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.
- 44. The method of claim 43, wherein the nucleic acid hybridization is performed using a nucleic acid probe.
- 45. The method of claim 43, wherein the nucleic acid hybridization is performed using a nucleic acid microarray.
- 46. The method of claim 43, wherein the nucleic acid amplification is performed using PCR.
- 47. The method of claim 38, wherein the therapeutic agent is an inhaled corticosteroid.
- 48. The method of claim 38, wherein the therapeutic agent is a bronchodilator.
- 49. The method of claim 38, wherein the COPD is selected from the group consisting of chronic bronchitis, emphysema, bronchioectasis and extrinsic allergic alveolitis.
- 50. The method of claim 38, wherein the subject has asthma.
- 51. The method of claim 38, wherein the presence of the sequence variation is indicative that the subject is not sensitive to the therapeutic agent.
- 52. The method of claim 38, further comprising assessing at least one risk factor to assess the sensitivity to the therapeutic agent.
- 53. The method of claim 52, wherein the risk factor is selected from the group consisting of baseline level of lung function, gender, age, race and prior steroid use.
- 54. A method of assessing sensitivity to a therapeutic agent in a subject with chronic obstructive pulmonary disease (COPD) or asthma, comprising:
detecting the presence of a nucleic acid molecule in a biological sample from the subject, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of a gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD1 IBI, HSD11B2, MAPK8, NFATC4, SCYA11 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-, which contains a sequence variation,
(a) nucleotide sequences set forth as SEQ ID NOs: 1-88, 122-308 and 325-374, and (b) fragments of (a), wherein the fragment of the nucleotide sequences contains a sequence variation, and wherein the presence of a sequence variation in the nucleic acid molecule is indicative of sensitivity to the therapeutic agent.
- 55. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 1-35 and fragments thereof, which contains a sequence variation.
- 56. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of CRHR1, and wherein the nucleotide sequence is selected from the group consisting of SEQ ID NOs: 205-208.
- 57. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of IL18BP, wherein the nucleotide sequence is selected from the group consisting of SEQ ID NOs: 209-212.
- 58. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of FCER2, wherein the nucleotide sequence is selected from the group consisting of SEQ ID NOs: 213-222.
- 59. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of CRHR1, wherein the sequence comprises the polymorphisms of rs1876828, rs242939 and rs242941.
- 60. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of IL18BP, wherein the sequence comprises the polymorphisms of rs1892919, G9772a3 and G9772a6.
- 61. The method of claim 54, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences of a region of FCER2, wherein the sequence comprises the polymorphisms of G9782a12, G9782a19, G9782a26, G9782a5 and G9782a8.
- 62. The method of claim 54, wherein the presence of the nucleic acid molecule is determined with a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.
- 63. The method of claim 62, wherein the nucleic acid hybridization is performed using a nucleic acid probe.
- 64. The method of claim 62, wherein the nucleic acid hybridization is performed using a nucleic acid microarray.
- 65. The method of claim 62, wherein the nucleic acid amplification is performed using PCR.
- 66. The method of claim 54, wherein the biological sample is a blood sample.
- 67. The method of claim 54, wherein the nucleic acid molecule is genomic DNA.
- 68. The method of claim 54, wherein the nucleic acid molecule is mRNA.
- 69. The method of claim 54, wherein the therapeutic agent is an inhaled corticosteroid.
- 70. The method of claim 54, wherein the therapeutic agent is a bronchodilator.
- 71. The method of claim 54, wherein the COPD is selected from the group consisting of chronic bronchitis, emphysema, bronchioectasis and extrinsic allergic alveolitis.
- 72. The method of claim 54, wherein the subject has asthma.
- 73. The method of claim 54, wherein the presence of the sequence variation is indicative that the subject is not sensitive to the therapeutic agent.
- 74. The method of claim 54, further comprising assessing at least one risk factor to assess the sensitivity to the therapeutic agent.
- 75. The method of claim 74, wherein the risk factor is selected from the group consisting of baseline level of lung function, gender, age, race and prior steroid use.
- 76. A method of assessing sensitivity to a therapeutic agent in a subject with a chronic obstructive pulmonary disease (COPD) or asthma, comprising:
determining the presence of a mutant protein encoded by a nucleic acid molecule selected from the group consisting of: nucleotide sequences of a region of a gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD11B1, HSD11B2, MAPK8, NFATC4, SCYA11 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-β, which contains a sequence variation,
(a) nucleotide sequences set forth as SEQ ID NOs: 1-88, 122-308 and 325-374, and (b) fragments of (b), which contain a sequence variation, wherein the presence of the mutant protein is indicative of sensitivity to the therapeutic agent.
- 77. The method of claim 76, wherein the nucleotide sequence is of a region of CRHR1, which contains a sequence variation.
- 78. The method of claim 76, wherein the nucleotide sequence is a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 79. The method of claim 76, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 1-35 and fragments thereof, which contain a sequence variation.
- 80. The method of claim 76, wherein the presence of the mutant protein is detected with an agent that selectively binds to the mutant protein.
- 81. The method of claim 80, wherein the agent that selectively binds is a binding polypeptide.
- 82. The method of claim 81, wherein the binding polypeptide is an antibody or an antigen-binding fragment thereof.
- 83. The method of claim 82, wherein the antibody is bound to a detectable label.
- 84. The method of claim 83, wherein the detectable label is a fluorescent molecule.
- 85. The method of claim 76, wherein the therapeutic agent is an inhaled corticosteroid.
- 77. A kit, comprising:
one or more nucleic acid probes that hybridize to at least one nucleic acid molecule selected from the group consisting of:
(a) nucleotide sequences of a region of a gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD11B1, HSD11B2, MAPK8, NFATC4, SCYA11 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-β, which contain a sequence variation, (b) nucleotide sequences set forth as SEQ ID NOs: 1-88, 122-308 and 325-374, and (c) fragments of (a), wherein the fragment of the nucleotide sequence contains a sequence variation, and instructions for the use of the nucleic acid probes to correlate the presence of the at least one nucleic acid molecule with sensitivity to a therapeutic agent.
- 78. The kit of claim 77, wherein the nucleotide sequence is of a region of CRHR1, which contains a sequence variation.
- 79. The kit of claim 77, wherein the nucleotide sequence is a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 80. The kit of claim 77, further comprising one or more control agents.
- 81. The kit of claim 77, wherein the one or more nucleic acidw consist of a first primer and a second primer, wherein the first primer and the second primer are constructed and arranged to selectively amplify a region of the nucleic acid molecule which contains a sequence variation.
- 82. The kit of claim 77 or 81, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 1-35.
- 83. The kit of claim 80, wherein the one or more nucleic acid probes and one or more control agents are bound to a substrate.
- 84. A kit, comprising:
one or more nucleic acid probes that hybridize to at least one nucleic acid molecule selected from the group consisting of:
(d) nucleotide sequences of a region of a NR3C1, which contain a sequence variation, (e) nucleotide sequences set forth as SEQ ID NOs: 89-121 and 309-324, and (f) fragments of (a), wherein the fragment of the nucleotide sequence contains a sequence variation, and instructions for the use of the nucleic acid probes to correlate the presence of the at least one nucleic acid molecule with sensitivity to a therapeutic agent.
- 85. The kit of claim 84, further comprising one or more control agents.
- 86. The kit of claim 84, wherein the at least one nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 89 and 100.
- 87. The kit of claim 84, wherein the one or more nucleic acid consist of a first primer and a second primer, wherein the first primer and the second primer are constructed and arranged to selectively amplify a region of the nucleic acid molecule which contains a sequence variation.
- 88. The kit of claim 84 or 87, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 89 and 100.
- 89. The kit of claim 85, wherein the one or more nucleic acid probes and one or more control agents are bound to a substrate.
- 90. A kit, comprising:
one or more nucleic acid probes that hybridize to at least one nucleic acid molecule selected from the group consisting of:
(g) nucleotide sequences of a region of a NR3C1, which contain a sequence variation, (h) nucleotide sequences set forth as SEQ ID NOs: 89-121 and 309-324, and (i) fragments of (a), wherein the fragment of the nucleotide sequence contains a sequence variation, and instructions for the use of the nucleic acid probes to correlate the presence of the at least one nucleic acid molecule with sensitivity to a therapeutic agent.
- 91. The kit of claim 90, further comprising one or more control agents.
- 92. The kit of claim 90, wherein the at least one nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 89 and 100.
- 93. The kit of claim 90, wherein the one or more nucleic acid consist of a first primer and a second primer, wherein the first primer and the second primer are constructed and arranged to selectively amplify a region of the nucleic acid molecule which contains a sequence variation.
- 94. The kit of claim 90 or 93, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 89 and 100.
- 95. The kit of claim 91, wherein the one or more nucleic acid probes and one or more control agents are bound to a substrate.
- 96. A kit, comprising:
one or more binding polypeptides that selectively bind to a mutant protein encoded by a nucleic acid molecule selected from the group consisting of:
(a) nucleotide sequences of a gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD11B1, HSD11B2, MAPK8, NFATC4, SCYA11 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-β, which contain a sequence variation, (b) nucleotide sequences set forth as SEQ ID NOs: 1-88, 122-308 and 325-374, and (c) fragments of (a) and (b), wherein the fragment of the nucleotide sequence contains a sequence variation, and instructions for the use of the one or more binding polypeptides to correlate the presence of the mutant protein with sensitivity to a therapeutic agent.
- 97. The kit of claim 96, wherein the nucleotide sequence is of a region of CRHR1, which contains a sequence variation.
- 98. The kit of claim 96, wherein the nucleotide sequence is a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 99. The kit of claim 96, further comprising one or more control agents.
- 100. The kit of claim 96, wherein the nucleic acid molecule is selected from the group consisting of nucleotide sequences set forth as SEQ ID NOs: 1-35 and fragments thereof, which contain a sequence variation.
- 101. The kit of claim 96, wherein the one or more binding polypeptides are antibodies or antigen-binding fragments thereof.
- 102. The kit of claim 101, wherein the antibodies or antigen-binding fragments thereof are bound to a substrate.
- 103. A nucleic acid microarray comprising at least two different nucleic acid molecules that hybridize to a nucleotide sequence selected from the group consisting of
(a) nucleotide sequences of a region of a gene selected from the group consisting of: ALOX15, CRH, CRHR1, CRHR2, urocortin, stresscopin, SRP (stresscopin-related peptide), CRHBP, EGR1, GATA3, HSD11B1, HSD11B2, MAPK8, NFATC4, SCYA11 (Eotaxin), FCER2 (CD23), IL18BP, ACTH (POMC), STAT3, STAT5A, STAT6, TBX21 (TBET) and TGF-β, which contain a sequence variation, (b) nucleotide sequences set forth as SEQ ID NOs: 1-88, 122-308 and 325-374 and (c) fragments of (a), wherein the fragment of the nucleotide sequence contains a sequence variation, and wherein the at least two nucleic acid molecules are fixed to a solid subtrate.
- 104. The nucleic acid microarray of claim 103, wherein the nucleotide sequence is of a region of CRHR1.
- 105. The nucleic acid microarray of claim 103, wherein the nucleotide sequence is a nucleotide sequence which comprises a polymorphism of rs1876828, rs242939 or rs242941.
- 106. The nucleic acid microarray of claim 103, wherein the nucleotide sequence is selected from the group consisting of nucleotide sequences set forth as: SEQ ID NOs: 1-35 and fragments thereof, which contain a sequence variation.
- 107. The nucleic acid microarray of claim 103, wherein at least ten different nucleic acid molecules are fixed to the solid substrate.
- 108. The nucleic acid microarray of any one of claims 103-107, further comprising at least one control nucleic acid molecule.
RELATED APPLICATIONS
[0001] This application claims the benefit under 35 U.S.C. § 119 of U.S. provisional application 60/416,969, filed Oct. 8, 2002, which is incorporated herein by reference.
GOVERNMENT SUPPORT
[0002] Aspects of the invention may have been made using funding from National Institutes of Health Grant number NIH HL65899. Accordingly, the Government may have rights in the invention.
Provisional Applications (1)
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Number |
Date |
Country |
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60416969 |
Oct 2002 |
US |