Claims
- 1. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes listed in Table 2, hybridized to nucleic acids derived from a cell suspected of being non-normal.
- 2. The array of claim 1 comprising 3-11 of the genes.
- 3. The array of claim 2 comprising 5-11 of the genes.
- 4. The array of claim 3 comprising all 11 genes.
- 5. The array of claim 1 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 6. The array of claim 1 wherein said cell is a human cell.
- 7. The array of claim 1 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 8. The array of claim 1 wherein at least one polynucleotide probe hybridizes to CRIP1 nucleic acid molecules.
- 9. The array of claim 1 wherein said non-normal cells are selected from ADH, DCIS, and IDC.
- 10. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes in Table 3, hybridized to nucleic acids derived from a cell suspected of being DCIS or IDC.
- 11. The array of claim 10 comprising 3-9 of the genes.
- 12. The array of claim 11 comprising 5-9 of the genes.
- 13. The array of claim 12 comprising all 9 genes.
- 14. The array of claim 10 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 15. The array of claim 10 wherein said cell is a human cell.
- 16. The array of claim 10 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 17. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes in Table 4, hybridized to nucleic acids derived from a cell suspected of being non-normal.
- 18. The array of claim 17 comprising 3-9 of the genes.
- 19. The array of claim 18 comprising 5-9 of the genes.
- 20. The array of claim 19 comprising all 9 genes.
- 21. The array of claim 17 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 22. The array of claim 17 wherein said cell is a human cell.
- 23. The array of claim 17 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 24. The array of claim 17 wherein at least one polynucleotide probe hybridizes to ELF5 nucleic acid molecules.
- 25. The array of claim 17 wherein said non-normal cells are selected from ADH, DCIS, and IDC
- 26. A method to determine the presence, grade or stage of breast cancer cells in a sample from a subject comprising assaying said sample for expression of one or more genes in Table 2 and/or one or more genes in Table 4.
- 27. The method of claim 26 wherein said assaying comprises preparing RNA from said sample.
- 28. The method of claim 27 wherein said RNA is used for quantitative PCR.
- 29. The method of claim 28 wherein said assaying comprises using an array.
- 30. The method of claim 26 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 31. The method of claim 30 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 32. The method of claim 26 wherein said non-normal cells are selected from ADH, DCIS, and IDC.
- 33. A method to determine the presence, grade or stage of breast cancer cells in a sample from a subject comprising
assaying said sample for expression of one or more genes selected from Table 2 and/or Table 4 and identifying said sample as containing non-normal breast cancer cells, optionally without grading by histomorphological criteria.
- 34. The method of claim 33 wherein said assaying comprises preparing RNA from said sample.
- 35. The method of claim 34 wherein said RNA is used for quantitative PCR.
- 36. The method of claim 33 wherein said assaying comprises using an array.
- 37. The method of claim 33 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 38. The method of claim 37 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 39. The method of claim 33 wherein said non-normal cells are selected from ADH, DCIS, and IDC.
- 40. A method to determine the presence of DCIS and/or IDC breast cancer cells of grade III in a sample from a subject comprising
assaying said sample for expression of one or more genes selected from Table 3, Table 6, and/or Table 9 and identifying said sample as containing breast cancer cells of grade III, optionally without grading by histomorphological criteria.
- 41. The method of claim 40 wherein said assaying comprises preparing RNA from said sample.
- 42. The method of claim 41 wherein said RNA is used for quantitative PCR.
- 43. The method of claim 40 wherein said assaying comprises using an array.
- 44. The method of claim 40 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 45. The method of claim 44 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 46. A method to determine the grade of either DCIS or IDC cancer progression in a sample from a subject comprising assaying said sample for expression of one or more genes listed in Table 10.
- 47. The method of claim 46 wherein said assaying comprises preparing RNA from said sample.
- 48. The method of claim 47 wherein said RNA is used for quantitative PCR.
- 49. The method of claim 46 wherein said assaying comprises using an array.
- 50. The method of claim 49 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 51. The method of claim 50 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 52. A method to determine the presence of DCIS and/or IDC breast cancer cells of grade I in a sample from a subject comprising
assaying said sample for expression of one or more genes selected from Table 7 and/or Table 8 and identifying said sample as containing breast cancer cells of grade I, optionally without grading by histomorphological criteria.
- 53. The method of claim 52 wherein said assaying comprises preparing RNA from said sample.
- 54. The method of claim 53 wherein said RNA is used for quantitative PCR.
- 55. The method of claim 52 wherein said assaying comprises using an array.
- 56. The method of claim 55 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 57. The method of claim 56 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 58. A method to determine the presence of DCIS and/or IDC breast cancer cells of grade I and/or grade III in a sample from a subject comprising assaying said sample for decreased expression of one or more genes selected from Table 5.
- 59. The method of claim 58 wherein said assaying comprises preparing RNA from said sample.
- 60. The method of claim 59 wherein said RNA is used for quantitative PCR.
- 61. The method of claim 58 wherein said assaying comprises using an array.
- 62. The method of claim 58 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 63. The method of claim 62 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 64. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes listed in Table 5, hybridized to nucleic acids derived from a cell suspected of being DCIS or IDC.
- 65. The array of claim 41 comprising 3-11 of the genes.
- 66. The array of claim 64 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 67. The array of claim 64 wherein said cell is a human cell.
- 68. The array of claim 64 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 69. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes listed in Table 6 and/or Table 9, hybridized to nucleic acids derived from a cell suspected of being grade III DCIS and/or IDC.
- 70. The array of claim 69 comprising 3-11 of the genes.
- 71. The array of claim 69 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 72. The array of claim 69 wherein said cell is a human cell.
- 73. The array of claim 69 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 74. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes listed in Table 7 and/or Table 8, hybridized to nucleic acids derived from a cell suspected of being grade I DCIS and/or IDC.
- 75. The array of claim 74 comprising 3-11 of the genes.
- 76. The array of claim 74 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 77. The array of claim 74 wherein said cell is a human cell.
- 78. The array of claim 74 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 79. An array comprising polynucleotide probes, capable of hybridizing to nucleic acid molecules of more than one of the genes listed in Table 10, hybridized to nucleic acids derived from a cell suspected of being DCIS or IDC.
- 80. The array of claim 79 comprising 3-11 of the genes.
- 81. The array of claim 79 wherein said cell is from a subject afflicted with, or suspected of having, breast cancer.
- 82. The array of claim 79 wherein said cell is a human cell.
- 83. The array of claim 79 wherein said nucleic acids derived from a cell are prepared by quantitative PCR.
- 84. A method to determine therapeutic treatment for a patient having cells suspected of being non-normal in a sample therefrom comprising
identifying said patient as having grade III DCIS and/or IDC after assaying said cells for expression of more than one gene listed in Table 3 and selecting the appropriate treatment for a patient having cells of such a grade.
- 85. The method of claim 84 wherein said assaying comprises preparing RNA from said cells.
- 86. The method of claim 85 wherein said RNA is used for quantitative PCR.
- 87. The method of claim 84 wherein said assaying comprises using an array.
- 88. The method of claim 87 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 89. The method of claim 88 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 90. The method of claim 84 wherein said non-normal cells are selected from ADH, DCIS, and IDC.
- 91. A method to determine therapeutic treatment for a patient having non-normal cells in a sample therefrom comprising
identifying said patient as having grade III DCIS and/or IDC after assaying said cells for expression of more than one gene listed in Table 6 and/or Table 9, and selecting the appropriate treatment for a patient having cells of such a grade.
- 92. The method of claim 91 wherein said assaying comprises preparing RNA from said cells.
- 93. The method of claim 92 wherein said RNA is used for quantitative PCR.
- 94. The method of claim 91 wherein said assaying comprises using an array.
- 95. The method of claim 91 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 96. The method of claim 95 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 97. The method of claim 91 wherein said non-normal cells are selected from ADH, DCIS, and IDC.
- 98. A method to determine therapeutic treatment for a patient having non-normal cells in a sample therefrom comprising
identifying said patient as having grade I DCIS and/or IDC after assaying said cells for expression of more than one gene listed in Table 7 and/or Table 8, and selecting the appropriate treatment for a patient having cells of such a grade.
- 99. The method of claim 98 wherein said assaying comprises preparing RNA from said cells.
- 100. The method of claim 99 wherein said RNA is used for quantitative PCR.
- 101. The method of claim 98 wherein said assaying comprises using an array.
- 102. The method of claim 98 wherein said sample is a ductal lavage or fine needle aspiration sample.
- 103. The method of claim 102 wherein said sample is microdissected to isolate one or more cells suspected of being breast cancer cells.
- 104. The method of claim 98 wherein said non-normal cells are selected from ADH, DCIS, and IDC.
RELATED APPLICATIONS
[0001] This application is a continuation-in-part of U.S. patent application Ser. No. 10/028,018 filed Dec. 21, 2001, which is hereby incorporated in its entirety as if fully set forth.
Continuation in Parts (1)
|
Number |
Date |
Country |
Parent |
10028018 |
Dec 2001 |
US |
Child |
10211015 |
Aug 2002 |
US |