US2003198972A1PendingUtilityA1
Grading of breast cancer
Priority: Dec 21, 2001Filed: Aug 1, 2002Published: Oct 23, 2003
Est. expiryDec 21, 2021(expired)· nominal 20-yr term from priority
C12Q 1/6886A61K 31/138C12Q 2600/112C12Q 2600/16C12Q 2600/158G01N 33/57595G01N 33/57515
62
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Claims
Abstract
Methods and compositions for the identification of breast cancer grade signatures are provided. The signature profiles are identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for identification of cells as being in one or more particular stages and/or grades of breast cancer.
Claims
exact text as granted — not AI-modifiedWe claim:
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.Join the waitlist — get patent alerts
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