Claims
- 1. An isolated polynucleotide comprising a nucleotide sequence chosen from the group consisting of:
a) a nucleotide sequence encoding the polypeptide given by SEQ ID NO:2 or SEQ ID NO:4; b) a nucleotide sequence complementary to a nucleotide sequence encoding the polypeptide given by SEQ ID NO:2 or SEQ ID NO:4; c) a nucleotide sequence encoding a polypeptide whose amino acid sequence is at least 90% identical to the amino acid sequence given by SEQ ID NO:2 or SEQ ID NO:4; d) a nucleotide sequence complementary to a nucleotide sequence encoding a polypeptide whose amino acid sequence is at least 90% identical to the amino acid sequence given by SEQ ID NO:2 or SEQ ID NO:4; e) a nucleotide sequence that is a fragment of any of the nucleotide sequences of a) through d); and f) a nucleotide sequence that hybridizes to a nucleotide sequence given by a) through e).
- 2. The polynucleotide described in paragraph e) of claim 1 wherein the fragment encodes a mature form of the polypeptide.
- 3. The polynucleotide described in claim 1 wherein the nucleotide sequence encodes the polypeptide given by SEQ ID NO:2 or SEQ ID NO:4, or wherein the nucleotide sequence is complementary to a nucleotide sequence encoding the polypeptide given by SEQ ID NO:2 or SEQ ID NO:4.
- 4. The polynucleotide described in claim 1 wherein the nucleotide sequence is given by SEQ ID NO:1, positions 43-918 of SEQ ID NO:1, or SEQ ID NO:3; or the complement to SEQ ID NO:1, positions 43-918 of SEQ ID NO:1, or SEQ ID NO:3.
- 5. The polynucleotide described in claim 1 wherein the polynucleotide is a RNA.
- 6. The polynucleotide described in claim 1 wherein the polynucleotide is a DNA.
- 7. The polynucleotide described in claim 1 wherein the nucleotide sequence encodes a peptide comprising at least 10 contiguous amino acids of the sequence from residue 225 to residue 240 of SEQ ID NO:2 or SEQ ID NO:4.
- 8. A vector comprising a polynucleotide sequence described in claim 1.
- 9. The vector described in claim 8 wherein the polynucleotide sequence is operably linked to provide for expression of the encoded polypeptide.
- 10. A host cell comprising the vector described in claim 9.
- 11. A pharmaceutical composition comprising a polynucleotide described in claim 1 and a pharmaceutically acceptable carrier.
- 12. A kit comprising a polynucleotide described in claim 1 placed within a container.
- 13. The kit described in claim 12 wherein the polynucleotide is comprised in a pharmaceutical composition.
- 14. The kit described in claim 12 wherein the polynucleotide is an antisense polynucleotide, a small inhibitory polynucleotide, or a micropolynucleotide.
- 15. The kit described in claim 14 wherein the polynucleotide is comprised in a pharmaceutical composition.
- 16. An isolated polypeptide comprising a sequence chosen from the group consisting of:
a) an amino acid sequence given by SEQ ID NO:2 or SEQ ID NO:4; b) a variant polypeptide whose amino acid sequence is at least 90% identical to the amino acid sequence given by SEQ ID NO:2 or SEQ ID NO:4; c) an amino acid sequence that is a fragment of any of the amino acid sequences given in a) and b).
- 17. The isolated polypeptide described in paragraph c) of claim 16 wherein the fragment is a mature form of the polypeptide.
- 18. The isolated polypeptide described in claim 16 wherein the amino acid sequence comprises at least 10 contiguous amino acids of the sequence from residue 225 to residue 240 of SEQ ID NO:2 or SEQ ID NO:4.
- 19. A method of preparing a polypeptide described in claim 16 comprising culturing a host cell described in claim 10 under conditions suitable for expression of the polypeptide, and isolating the polypeptide.
- 20. The method described in claim 19 wherein the vector comprises a polynucleotide sequence encoding the amino acid sequence given by SEQ ID NO:2 or SEQ ID NO:4.
- 21. An antibody that binds immunospecifically to a polypeptide described in claim 16.
- 22. The antibody described in claim 21 wherein the antibody binds immunospecifically to a polypeptide described in claim 18.
- 23. The antibody described in claim 21 wherein the antibody is a polyclonal antibody, a monoclonal antibody, a humanized antibody, or a fully human antibody.
- 24. A kit comprising the antibody described in claim 21 placed in a container.
- 25. A method of detecting the presence of or quantifying the amount of an Oncoseq polynucleotide in a sample comprising the steps of:
a) providing a sample comprising sample nucleic acid; and b) detecting the presence of or quantifying the amount of an Oncoseq polynucleotide in the sample nucleic acid.
- 26. The method described in claim 25 wherein a target nucleotide sequence that comprises at least a portion of the Oncoseq sequence in the sample nucleic is expanded, and wherein the detecting or quantifying in step b) is performed on the expanded target Oncoseq sequence.
- 27. The method described in claim 26 wherein the expanding comprises reverse transcription or a polymerase chain reaction, or both.
- 28. The method described in claim 25 wherein the detecting or quantifying in step b) comprises fluorescence in situ hybridization or a real-time polymerase chain reaction.
- 29. The method described in claim 25 wherein the detecting or quantifying in step b) comprises contacting the sample nucleic acid with a probe nucleic acid comprising a polynucleotide described in claim 1 that hybridizes to an Oncoseq polynucleotide under conditions that assure specific hybridization of the Oncoseq polynucleotide to the probe, and detecting the presence of or quantifying the amount of the Oncoseq polynucleotide that hybridizes to the probe nucleic acid.
- 30. The method described in claim 25 wherein the Oncoseq polynucleotide comprises a label, and wherein the detecting or quantifying comprises detecting or quantifying the label.
- 31. The method described in claim 29 wherein the probe nucleic acid is bound to a solid surface.
- 32. A method of determining whether the copy number of an Oncoseq sequence in a sample differs from the copy number of the Oncoseq sequence in a reference, wherein the method comprises the steps of:
a) providing a sample having sample nucleic acid comprising the Oncoseq sequence; b) detecting whether the amount of the Oncoseq sequence in the sample nucleic acid differs from the amount of the Oncoseq sequence in a reference nucleic acid comprising the Oncoseq sequence; whereby finding that the amounts differ determines that the copy number of the Oncoseq sequence in the sample differs from the copy number of the Oncoseq sequence in the reference.
- 33. The method described in claim 32 wherein the sample nucleic acid and the reference nucleic acid each comprise DNA.
- 34. The method described in claim 32 wherein the sample nucleic acid and the reference nucleic acid each comprise RNA.
- 35. The method described in claim 32 wherein the sample is provided from a mammal and the reference is provided from the same species of mammal.
- 36. The method described in claim 32 wherein the sample is provided from a human and the reference is provided from a human.
- 37. The method described in claim 32 wherein the sample comprises a cancer cell and the reference does not comprise a cancer cell.
- 38. The method described in claim 32 wherein a target nucleotide sequence that comprises at least a portion of the Oncoseq sequence in the sample nucleic acid and in the reference nucleic acid are separately expanded prior to the detecting in step b), and wherein the detecting is performed on the expanded target Oncoseq sequence in the sample nucleic acid and on the expanded target Oncoseq sequence in the reference nucleic acid.
- 39. The method described in claim 38 wherein the expanding comprises reverse transcription or a polymerase chain reaction, or both.
- 40. The method described in claim 32 wherein each Oncoseq sequence comprises a label, and wherein the detecting comprises detecting the label.
- 41. The method described in claim 32 wherein detecting the amounts in step b) comprises fluorescence in situ hybridization or a real-time polymerase chain reaction.
- 42. The method described in claim 32 wherein the detecting in step b) comprises separately contacting the sample nucleic acid and the reference nucleic acid with a probe nucleic acid comprising a polynucleotide described in claim 1 that hybridizes to an Oncoseq polynucleotide under conditions that assure specific hybridization of the Oncoseq polynucleotide to the probe, and detecting the amount of the Oncoseq polynucleotide in the sample nucleic acid and in the reference nucleic acid that hybridize to the probe nucleic acid.
- 43. The method described in claim 42 wherein the probe nucleic acid is bound to a solid surface.
- 44. A method of contributing to the diagnosis or prognosis of, or to developing a therapeutic strategy for, a pathology in a first subject, wherein the copy number of an Oncoseq sequence in the pathology is known to differ from the copy number of the Oncoseq sequence in a nonpathological state, the method comprising the steps of:
a) providing a sample from the first subject comprising sample nucleic acid, wherein the sample nucleic acid includes the Oncoseq sequence; b) determining whether the amount of the Oncoseq sequence in the sample nucleic acid differs from the amount of the Oncoseq sequence in a reference nucleic acid, wherein the reference nucleic acid is from a reference from a second subject known not to have the pathology and wherein the reference nucleic acid includes the Oncoseq sequence; and c) determining that the copy number of the Oncoseq sequence in the first subject differs from the copy number of the Oncoseq sequence in the second subject when the amounts detected in step b) differ from each other; thus contributing to the diagnosis of, prognosis of, or developing a therapeutic strategy for, the pathology.
- 45. The method described in claim 44 wherein the sample nucleic acid and the reference nucleic acid each comprise DNA.
- 46. The method described in claim 44 wherein the sample nucleic acid and the reference nucleic acid each comprise RNA.
- 47. The method described in claim 44 wherein the pathology is a cancer, a tumor, a carcinoma, a sarcoma, a blastoma, a lymphoma, a leukemia, or a neoplastic disease.
- 48. The method described in claim 44 wherein the sample is provided from a mammal and the reference is provided from the same species of mammal.
- 49. The method described in claim 44 wherein the sample is provided from a human and the reference is provided from a human.
- 50. The method described in claim 44 wherein the sample comprises a cancer cell and the reference does not comprise a cancer cell.
- 51. The method described in claim 44 wherein a target nucleotide sequence that comprises at least a portion of the Oncoseq sequence in the sample nucleic and in the reference nucleic acid are separately expanded prior to the detecting in step b), and wherein the detecting is performed on the expanded target Oncoseq sequence in the sample nucleic acid and on the expanded target Oncoseq sequence in the reference nucleic acid.
- 52. The method described in claim 51 wherein the expanding comprises reverse transcription or a polymerase chain reaction, or both.
- 53. The method described in claim 44 wherein each Oncoseq sequence is labeled, and wherein the determining comprises detecting the label.
- 54. The method described in claim 44 wherein detecting the amounts in step b) comprises fluorescence in situ hybridization or a real-time polymerase chain reaction.
- 55. The method described in claim 44 wherein the detecting in step b) comprises separately contacting the sample nucleic acid and the reference nucleic acid with a probe nucleic acid comprising a polynucleotide described in claim 1 that hybridizes to an Oncoseq polynucleotide under conditions that assure specific hybridization of the Oncoseq polynucleotide to the probe, and detecting the amount of the Oncoseq polynucleotide in the sample nucleic acid and in the reference nucleic acid that hybridize to the probe nucleic acid.
- 56. The method described in claim 44 wherein the probe nucleic acid is bound to a solid surface.
- 57. A method of detecting the presence or quantifying the amount of an Oncoseq polypeptide in a sample comprising the steps of:
a) providing a sample comprising sample polypeptides wherein the sample polypeptides are suspected to include the Oncoseq polypeptide; b) contacting the polypeptide with a specific binding agent that binds a polypeptide described in claim 16 under conditions that assure binding of the Oncoseq polypeptide to the specific binding agent; and c) detecting the presence or quantifying the amount of the specific binding agent that binds to the Oncoseq polypeptide.
- 58. The method described in claim 57 wherein the specific binding agent comprises a label, or wherein the specific binding agent binds a secondary binding agent that comprises a label, and wherein the detecting or the quantifying comprises detecting or quantifying the label.
- 59. The method described in claim 57 wherein after step a) the Oncoseq polypeptide is bound to a solid surface.
- 60. The method described in claim 57 wherein the specific binding agent is an antibody described in claim 21.
- 61. A method of determining whether the amount of an Oncoseq polypeptide in a sample differs from the amount of the Oncoseq polypeptide in a reference, wherein the method comprises the steps of:
a) providing a sample suspected to include the Oncoseq polypeptide; b) contacting the sample with a specific binding agent that binds a polypeptide described in claim 16 under conditions that assure binding of the Oncoseq polypeptide to the specific binding agent; and c) determining whether the amount of the specific binding agent that binds to the sample differs from the amount of the specific binding agent that binds to a reference, wherein the reference is prepared by providing a reference comprising a standard or reference amount of the Oncoseq polypeptide, and contacting the reference with the specific binding agent used in step b) under the same conditions used in step b).
- 62. The method described in claim 61 wherein the sample is provided from a human and the reference is provided from a human.
- 63. The method described in claim 61 wherein the sample is provided from a mammal and the reference is provided from the same species of mammal.
- 64. The method described in claim 61 wherein the sample comprises a cancer cell and the reference does not comprise a cancer cell.
- 65. The method described in claim 61 wherein the specific binding agent comprises a label, or wherein the specific binding agent binds a secondary binding agent that comprises a label, and wherein the determining comprises detecting the label.
- 66. The method described in claim 61 wherein after step a) separately the Oncoseq polypeptide in the sample polypeptides and the Oncoseq polypeptide in the reference polypeptides is bound to a solid surface.
- 67. The method described in claim 61 wherein the specific binding agent is an antibody described in claim 21.
- 68. A method of contributing to the diagnosis or prognosis of, or to developing a therapeutic strategy for, a pathology in a first subject, wherein the amount of an Oncoseq polypeptide in the pathology is known to differ from the amount of the Oncoseq polypeptide in a nonpathological state, the method comprising the steps of:
a) providing a sample from the first subject suspected to include the Oncoseq polypeptide; b) contacting the sample with a specific binding agent that binds a polypeptide described in claim 16 under conditions that assure binding of the Oncoseq polypeptide to the specific binding agent; and c) determining whether the amount of the specific binding agent that binds to the sample differs from the amount of the specific binding agent that binds to a reference, wherein the reference is provided from a second subject known not to have the pathology and wherein the reference includes the Oncoseq polypeptide, and contacting the reference with the specific binding agent used in step b) under the same conditions used in step b); thus contributing to the diagnosis or prognosis of, or to developing a therapeutic strategy for, the pathology.
- 69. The method described in claim 68 wherein the pathology is a cancer, a tumor, a carcinoma, a sarcoma, a blastoma, a lymphoma, a leukemia, or a neoplastic disease.
- 70. The method described in claim 68 wherein the sample is provided from a mammal and the reference is provided from the same species of mammal.
- 71. The method described in claim 68 wherein the sample is provided from a human and the reference is provided from a human.
- 72. The method described in claim 68 wherein the sample comprises a cancer cell and the reference does not comprise a cancer cell.
- 73. The method described in claim 68 wherein the specific binding agent comprises a label, or wherein the specific binding agent binds a secondary binding agent that comprises a label, and wherein the determining comprises detecting the label.
- 74. The method described in claim 68 wherein after step a) separately the Oncoseq polypeptide in the sample polypeptides and the Oncoseq polypeptide in the reference polypeptides is bound to a solid surface.
- 75. The method described in claim 68 wherein the specific binding agent is an antibody described in claim 21.
- 76. A method of inhibiting the growth of a cell comprising contacting the cell with a composition that lowers expression of an Oncoseq nucleotide sequence in the cell.
- 77. The method described in claim 76 wherein the composition comprises a polynucleotide described in claim 1.
- 78. The method described in claim 76 wherein the copy number of the Oncoseq gene in the cell is pathologically high.
- 79. A method of inhibiting the growth of a cell in a sample, wherein the cell has a copy number of an Oncoseq gene characteristic of a pathology, the method comprising contacting the cell with a composition comprising a polynucleotide described in claim 1 or a polypeptide described in claim 16.
- 80. The method described in claim 79 wherein the sample is located in a human subject.
- 81. The method described in claim HC wherein the composition comprises a polynucleotide that comprises an antisense polynucleotide, a small inhibitory polynucleotide, or a micro polynucleotide.
- 82. The method described in claim 79 wherein the composition interferes with the activity of an Oncoseq gene or an Oncoseq polypeptide.
- 83. The method described in claim 82 wherein the composition is a polypeptide that comprises a fragment described in claim 16.
- 84. The method described in claim 83 wherein the fragment comprises an amino acid sequence beginning at residue 136 and ending at residue 245 of SEQ ID NO:2 or SEQ ID NO:4.
- 85. The method described in claim 79 wherein the pathology is a cancer, a tumor, a carcinoma, a sarcoma, a blastoma, a lymphoma, a leukemia, or a neoplastic disease.
- 86. The method described in claim 79 wherein the pathology is a squamous cell carcinoma.
RELATED APPLICATION
[0001] This application claims the benefit of priority of U.S. Ser. No. 60/355, 009, filed Feb. 8, 2002, the contents of which are incorporated herein in their entirety.
Provisional Applications (1)
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Number |
Date |
Country |
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60355009 |
Feb 2002 |
US |