Patent Application

App. No. 14/772,348

Abstract

Claims (208)

1 . A method of diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy in a subject, comprising:

(a) assaying an expression level in a sample from the subject for a plurality of targets, wherein the plurality of targets comprises one or more targets selected from Table 1; and

(b) diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy in a subject based on the expression levels of the plurality of targets.

2 . A method of determining a treatment for a cancer in a subject, comprising:

(a) assaying an expression level in a sample from the subject for a plurality of targets, wherein the plurality of targets comprises one or more targets selected from Table 1; and

(b) determining the treatment for the cancer based on the expression level of the plurality of targets.

3 . The method of any of claims 1 - 2 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

4 . The method of any of claims 1 - 2 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

5 . The method of any of claims 1 - 2 , wherein the cancer is a prostate cancer.

6 . The method of any of claims 1 - 2 , wherein the cancer is a pancreatic cancer.

7 . The method of any of claims 1 - 2 , wherein the cancer is a thyroid cancer.

8 . The method of any of claims 1 - 2 , wherein the plurality of targets comprises a coding target.

9 . The method of claim 8 , wherein the coding target is an exonic sequence.

10 . The method of any of claims 1 - 2 , wherein the plurality of targets comprises a non-coding target.

11 . The method of claim 10 , wherein the non-coding target comprises an intronic sequence or partially overlaps an intronic sequence.

12 . The method of claim 10 , wherein the non-coding target comprises a sequence within the UTR or partially overlaps with a UTR sequence.

13 . The method of any of claims 1 - 2 , wherein the target comprises a nucleic acid sequence.

14 . The method of claim 13 , wherein the nucleic acid sequence is a DNA sequence.

15 . The method of claim 13 , wherein the nucleic acid sequence is an RNA sequence.

16 . The method of any of claims 1 - 2 , wherein the plurality of targets comprises at least 5 targets selected from Table 1.

17 . The method of any of claims 1 - 2 , wherein the plurality of targets comprises at least 10 targets selected from Table 1.

18 . The method of any of claims 1 - 2 , wherein the plurality of targets comprises at least 15 targets selected from Table 1.

19 . The method of any of claims 1 - 2 , wherein the plurality of targets comprises at least 20 targets selected from Table 1.

20 . The method of claim 1 , wherein the diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy includes determining the malignancy of the cancer.

21 . The method of claim 1 , wherein the diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy includes determining the stage of the cancer.

22 . The method of claim 1 , wherein the diagnosing, prognosing, determining progression the cancer, or predicting benefit from therapy includes assessing the risk of cancer recurrence.

23 . The method of claim 2 , wherein determining the treatment for the cancer includes determining the efficacy of treatment.

24 . The method of any of claims 1 - 2 , further comprising sequencing the plurality of targets.

25 . The method of any of claims 1 - 2 , further comprising hybridizing the plurality of targets to a solid support.

26 . The method of claim 25 , wherein the solid support is a bead or array.

27 . A probe set for assessing a cancer status of a subject comprising a plurality of probes, wherein the probes in the set are capable of detecting an expression level of one or more targets selected from Table 1, wherein the expression level determines the cancer status of the subject with at least 40% specificity.

28 . The probe set of claim 27 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

29 . The probe set of claim 27 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

30 . The probe set of claim 27 , wherein the cancer is a prostate cancer.

31 . The probe set of claim 27 , wherein the cancer is a pancreatic cancer.

32 . The probe set of claim 27 , wherein the cancer is a thyroid cancer.

33 . The probe set of claim 27 , wherein the probe set further comprises a probe capable of detecting an expression level of at least one coding target.

34 . The probe set of claim 33 , wherein the coding target is an exonic sequence.

35 . The probe set of claim 27 , wherein the probe set further comprises a probe capable of detecting an expression level of at least one non-coding target.

36 . The probe set of claim 35 , wherein the non-coding target is an intronic sequence or partially overlaps with an intronic sequence.

37 . The probe set of claim 35 , wherein the non-coding target is a UTR sequence or partially overlaps with a UTR sequence.

38 . The probe set of claim 27 , wherein assessing the cancer status includes assessing cancer recurrence risk.

39 . The probe set of claim 27 , wherein assessing the cancer status includes determining a treatment modality.

40 . The probe set of claim 27 , wherein assessing the cancer status includes determining the efficacy of treatment.

41 . The probe set of claim 27 , wherein the target is a nucleic acid sequence.

42 . The probe set of claim 41 , wherein the nucleic acid sequence is a DNA sequence.

43 . The probe set of claim 41 , wherein the nucleic acid sequence is an RNA sequence.

44 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 500 nucleotides in length.

45 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 450 nucleotides in length.

46 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 400 nucleotides in length.

47 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 350 nucleotides in length.

48 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 300 nucleotides in length.

49 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 250 nucleotides in length.

50 . The probe set of claim 27 , wherein the probes are between about 15 nucleotides and about 200 nucleotides in length.

51 . The probe set of claim 27 , wherein the probes are at least 15 nucleotides in length.

52 . The probe set of claim 27 , wherein the probes are at least 25 nucleotides in length.

53 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 50% specificity.

54 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 60% specificity.

55 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 65% specificity.

56 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 70% specificity.

57 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 75% specificity.

58 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 80% specificity.

59 . The probe set of claim 27 , wherein the expression level determines the cancer status of the subject with at least 85% specificity.

60 . The probe set of claim 27 , wherein the non-coding target is a non-coding RNA transcript and the non-coding RNA transcript is non-polyadenylated.

61 . A system for analyzing a cancer, comprising:

(a) a probe set comprising a plurality of target sequences, wherein

(i) the plurality of target sequences hybridizes to one or more targets selected from Table 1; or

(ii) the plurality of target sequences comprises one or more target sequences selected from Table 1; and

(b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target hybridized to the probe in a sample from a subject suffering from a cancer.

62 . The system of claim 61 , further comprising an electronic memory for capturing and storing an expression profile.

63 . The system of claim 61 or claim 62 , further comprising a computer-processing device, optionally connected to a computer network.

64 . The system of claim 63 , further comprising a software module executed by the computer-processing device to analyze an expression profile.

65 . The system of claim 63 , further comprising a software module executed by the computer-processing device to compare the expression profile to a standard or control.

66 . The system of claim 63 , further comprising a software module executed by the computer-processing device to determine the expression level of the target.

67 . The system of any claims 61 - 66 , further comprising a machine to isolate the target or the probe from the sample.

68 . The system of any claims 61 - 67 , further comprising a machine to sequence the target or the probe.

69 . The system of any claims 61 - 68 , further comprising a machine to amplify the target or the probe.

70 . The system of any claims 61 - 69 , further comprising a label that specifically binds to the target, the probe, or a combination thereof.

71 . The system of claim 63 , further comprising a software module executed by the computer-processing device to transmit an analysis of the expression profile to the individual or a medical professional treating the individual.

72 . The system of any claims 61 - 71 , further comprising a software module executed by the computer-processing device to transmit a diagnosis or prognosis to the individual or a medical professional treating the individual.

73 . The system of any claims 61 - 72 , wherein the plurality of target sequences comprises at least 5 target sequences selected from Table 1.

74 . The system of any claims 61 - 72 , wherein the plurality of target sequences comprises at least 10 target sequences selected from Table 1.

75 . The system of any claims 61 - 72 , wherein the plurality of target sequences comprises at least 15 target sequences selected from Table 1.

76 . The system of any claims 61 - 72 , wherein the plurality of target sequences comprises at least 20 target sequences selected from Table 1.

77 . The system of any claims 61 - 76 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

78 . The system of any claims 61 - 76 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

79 . A method of analyzing a cancer in an individual in need thereof, comprising:

(a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 1; and

(b) comparing the expression profile from the sample to an expression profile of a control or standard.

80 . The method of claim 79 , wherein the plurality of targets comprises at least 5 targets selected from Table 1.

81 . The method of claim 79 , wherein the plurality of targets comprises at least 10 targets selected from Table 1.

82 . The method of claim 79 , wherein the plurality of targets comprises at least 15 targets selected from Table 1.

83 . The method of claim 79 , wherein the plurality of targets comprises at least 20 targets selected from Table 1.

84 . The method of any of claims 79 - 83 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

85 . The method of any of claims 79 - 83 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

86 . The method of any of claims 79 - 85 , further comprising a software module executed by a computer-processing device to compare the expression profiles.

87 . The method of any of claims 79 - 86 , further comprising providing diagnostic or prognostic information to the individual about the cardiovascular disorder based on the comparison.

88 . The method of any of claims 79 - 87 , further comprising diagnosing the individual with a cancer if the expression profile of the sample (a) deviates from the control or standard from a healthy individual or population of healthy individuals, or (b) matches the control or standard from an individual or population of individuals who have or have had the cancer.

89 . The method of any of claims 79 - 88 , further comprising predicting the susceptibility of the individual for developing a cancer based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (b) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

90 . The method of any of claims 79 - 89 , further comprising prescribing a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (b) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

91 . The method of any of claims 79 - 90 , further comprising altering a treatment regimen prescribed or administered to the individual based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (b) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

92 . The method of any of claims 79 - 91 , further comprising predicting the individual's response to a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (b) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

93 . The method of any of claims 89 - 92 , wherein the deviation is the expression level of one or more targets from the sample is greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

94 . The method of any of claims 89 - 92 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

95 . The method of any of claims 89 - 90 , wherein the deviation is the expression level of one or more targets from the sample is less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

96 . The method of any of claims 89 - 92 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

97 . The method of any of claims 79 - 96 , further comprising using a machine to isolate the target or the probe from the sample.

98 . The method of any of claims 79 - 97 , further comprising contacting the sample with a label that specifically binds to the target, the probe, or a combination thereof.

99 . The method of any of claims 79 - 98 , further comprising contacting the sample with a label that specifically binds to a target selected from Table 1.

100 . The method of any of claims 79 - 99 , further comprising amplifying the target, the probe, or any combination thereof.

101 . The method of any of claims 79 - 100 , further comprising sequencing the target, the probe, or any combination thereof.

102 . A method of diagnosing cancer in an individual in need thereof, comprising:

(a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 1;

(b) comparing the expression profile from the sample to an expression profile of a control or standard; and

(c) diagnosing a cancer in the individual if the expression profile of the sample (i) deviates from the control or standard from a healthy individual or population of healthy individuals, or (ii) matches the control or standard from an individual or population of individuals who have or have had the cancer.

103 . The method of claim 102 , wherein the plurality of targets comprises at least 5 targets selected from Table 1.

104 . The method of claim 102 , wherein the plurality of targets comprises at least 10 targets selected from Table 1.

105 . The method of claim 102 , wherein the plurality of targets comprises at least 15 targets selected from Table 1.

106 . The method of claim 102 , wherein the plurality of targets comprises at least 20 targets selected from Table 1.

107 . The method of any of claims 102 - 106 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

108 . The method of any of claims 102 - 106 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

109 . The method of any of claims 102 - 108 , further comprising a software module executed by a computer-processing device to compare the expression profiles.

110 . The method of any of claims 102 - 109 , wherein the deviation is the expression level of one or more targets from the sample is greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

111 . The method of any of claims 102 - 109 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

112 . The method of any of claims 102 - 109 , wherein the deviation is the expression level of one or more targets from the sample is less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

113 . The method of any of claims 102 - 109 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

114 . The method of any of claims 102 - 113 , further comprising using a machine to isolate the target or the probe from the sample.

115 . The method of any of claims 102 - 114 , further comprising contacting the sample with a label that specifically binds to the target, the probe, or a combination thereof.

116 . The method of any of claims 102 - 115 , further comprising contacting the sample with a label that specifically binds to a target selected from Table 1.

117 . The method of any of claims 102 - 116 , further comprising amplifying the target, the probe, or any combination thereof.

118 . The method of any of claims 102 - 117 , further comprising sequencing the target, the probe, or any combination thereof.

119 . A method of predicting whether an individual is susceptible to developing a cancer, comprising:

(a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 1;

(b) comparing the expression profile from the sample to an expression profile of a control or standard; and

(c) predicting the susceptibility of the individual for developing a cancer based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

120 . The method of claim 119 , wherein the plurality of targets comprises at least 5 targets selected from Table 1.

121 . The method of claim 119 , wherein the plurality of targets comprises at least 10 targets selected from Table 1.

122 . The method of claim 119 , wherein the plurality of targets comprises at least 15 targets selected from Table 1.

123 . The method of claim 119 , wherein the plurality of targets comprises at least 20 targets selected from Table 1.

124 . The method of any of claims 119 - 123 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

125 . The method of any of claims 119 - 123 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

126 . The method of any of claims 119 - 125 , further comprising a software module executed by a computer-processing device to compare the expression profiles.

127 . The method of any of claims 119 - 126 , wherein the deviation is the expression level of one or more targets from the sample is greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

128 . The method of any of claims 119 - 126 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

129 . The method of any of claims 119 - 126 , wherein the deviation is the expression level of one or more targets from the sample is less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

130 . The method of any of claims 119 - 126 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

131 . The method of any of claims 119 - 130 , further comprising using a machine to isolate the target or the probe from the sample.

132 . The method of any of claims 119 - 131 , further comprising contacting the sample with a label that specifically binds to the target, the probe, or a combination thereof.

133 . The method of any of claims 119 - 132 , further comprising contacting the sample with a label that specifically binds to a target selected from Table 1.

134 . The method of any of claims 119 - 133 , further comprising amplifying the target, the probe, or any combination thereof.

135 . The method of any of claims 119 - 134 , further comprising sequencing the target, the probe, or any combination thereof.

136 . A method of predicting an individual's response to a treatment regimen for a cancer, comprising:

(a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 1;

(b) comparing the expression profile from the sample to an expression profile of a control or standard; and

(c) predicting the individual's response to a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (b) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

137 . The method of claim 136 , wherein the plurality of targets comprises at least 5 targets selected from Table 1.

138 . The method of claim 136 , wherein the plurality of targets comprises at least 10 targets selected from Table 1.

139 . The method of claim 136 , wherein the plurality of targets comprises at least 15 targets selected from Table 1.

140 . The method of claim 136 , wherein the plurality of targets comprises at least 20 targets selected from Table 1.

141 . The method of any of claims 136 - 140 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

142 . The method of any of claims 136 - 140 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

143 . The method of any of claims 136 - 142 , further comprising a software module executed by a computer-processing device to compare the expression profiles.

144 . The method of any of claims 136 - 143 , wherein the deviation is the expression level of one or more targets from the sample is greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

145 . The method of any of claims 136 - 143 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

146 . The method of any of claims 136 - 143 , wherein the deviation is the expression level of one or more targets from the sample is less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

147 . The method of any of claims 136 - 143 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

148 . The method of any of claims 136 - 147 , further comprising using a machine to isolate the target or the probe from the sample.

149 . The method of any of claims 136 - 148 , further comprising contacting the sample with a label that specifically binds to the target, the probe, or a combination thereof.

150 . The method of any of claims 136 - 149 , further comprising contacting the sample with a label that specifically binds to a target selected from Table 1.

151 . The method of any of claims 136 - 150 , further comprising amplifying the target, the probe, or any combination thereof.

152 . The method of any of claims 136 - 151 , further comprising sequencing the target, the probe, or any combination thereof.

153 . A method of prescribing a treatment regimen for a cancer to an individual in need thereof, comprising:

(a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 1;

(b) comparing the expression profile from the sample to an expression profile of a control or standard; and

(c) prescribing a treatment regimen based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

154 . The method of claim 153 , wherein the plurality of targets comprises at least 5 targets selected from Table 1.

155 . The method of claim 153 , wherein the plurality of targets comprises at least 10 targets selected from Table 1.

156 . The method of claim 153 , wherein the plurality of targets comprises at least 15 targets selected from Table 1.

157 . The method of claim 153 , wherein the plurality of targets comprises at least 20 targets selected from Table 1.

158 . The method of any of claims 153 - 157 , wherein the cancer is selected from the group consisting of a carcinoma, sarcoma, leukemia, lymphoma, myeloma, and a CNS tumor.

159 . The method of any of claims 153 - 157 , wherein the cancer is selected from the group consisting of skin cancer, lung cancer, colon cancer, pancreatic cancer, prostate cancer, liver cancer, thyroid cancer, ovarian cancer, uterine cancer, breast cancer, cervical cancer, kidney cancer, epithelial carcinoma, squamous carcinoma, basal cell carcinoma, melanoma, papilloma, and adenomas.

160 . The method of any of claims 153 - 159 , further comprising a software module executed by a computer-processing device to compare the expression profiles.

161 . The method of any of claims 153 - 160 , wherein the deviation is the expression level of one or more targets from the sample is greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

162 . The method of any of claims 153 - 160 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

163 . The method of any of claims 153 - 160 , wherein the deviation is the expression level of one or more targets from the sample is less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

164 . The method of any of claims 153 - 160 , wherein the deviation is the expression level of one or more targets from the sample is at least about 30% less than the expression level of one or more targets from a control or standard derived from a healthy individual or population of healthy individuals.

165 . The method of any of claims 153 - 164 , further comprising using a machine to isolate the target or the probe from the sample.

166 . The method of any of claims 153 - 165 , further comprising contacting the sample with a label that specifically binds to the target, the probe, or a combination thereof.

167 . The method of any of claims 153 - 166 , further comprising contacting the sample with a label that specifically binds to a target selected from Table 1.

168 . The method of any of claims 153 - 167 , further comprising amplifying the target, the probe, or any combination thereof.

169 . The method of any of claims 153 - 168 , further comprising sequencing the target, the probe, or any combination thereof.

170 . The method of claim 153 - 169 , further comprising converting the expression levels of the target sequences into a likelihood score that indicates the probability that a biological sample is from a patient who will exhibit no evidence of disease, who will exhibit systemic cancer, or who will exhibit biochemical recurrence.

171 . The method of claim 153 - 170 , wherein the target sequences are differentially expressed the cancer.

172 . The method of claim 171 , wherein the differential expression is dependent on aggressiveness.

173 . The method of claim 153 - 172 , wherein the expression profile is determined by a method selected from the group consisting of RT-PCR, Northern blotting, ligase chain reaction, array hybridization, and a combination thereof.

174 . A kit for analyzing a cancer, comprising:

(a) a probe set comprising a plurality of target sequences, wherein the plurality of target sequences comprises at least one target sequence listed in Table 1; and

(b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target sequences in a sample.

175 . The kit of claim 174 , further comprising a computer model or algorithm for correlating the expression level or expression profile with disease state or outcome.

176 . The kit of claim 174 , further comprising a computer model or algorithm for designating a treatment modality for the individual.

177 . The kit of claim 174 , further comprising a computer model or algorithm for normalizing expression level or expression profile of the target sequences.

178 . The kit of claim 174 , further comprising a computer model or algorithm comprising a robust multichip average (RMA), probe logarithmic intensity error estimation (PLIER), non-linear fit (NLFIT) quantile-based, nonlinear normalization, or a combination thereof.

179 . The kit of claim 174 , wherein the cancer is a prostate cancer.

180 . The kit of claim 174 , wherein the cancer is a lung cancer.

181 . The kit of claim 174 , wherein the cancer is a breast cancer.

182 . The kit of claim 174 , wherein the cancer is a thyroid cancer.

183 . The kit of claim 174 , wherein the cancer is a colon cancer.

184 . The kit of claim 174 , wherein the cancer is a pancreatic cancer.

Assignments (8)