IP Library › Patent Application 15765711

Patent Application

App. No. 15/765,711

USE OF A GENETIC SIGNATURE DIAGNOSTICALLY TO EVALUATE TREATMENT STRATEGIES FOR PROSTATE CANCER

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App. No.: 15/765,711

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Abstract

Methods, compositions, and kits for identifying individuals who will be resistant to androgen deprivation therapy for treatment of prostate cancer are disclosed. In particular, the invention relates to an androgen deprivation therapy resistance signature based on expression levels of genes that are differentially expressed between responders and non-responders to androgen deprivation therapy and its use to identify individuals likely to respond poorly or be non-responsive to androgen deprivation therapy, who are in need of treatment for prostate cancer by other methods.

Claims (112)

1 . A diagnostic method for predicting resistance to androgen deprivation therapy (ADT) for a subject who has prostate cancer, the method comprising:

a) measuring the level of expression of a plurality of biomarker genes comprising SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12, NLRP13, MPP7, CFL1, DESI2, OR51E2, KCNMB1, DLGAP1, SPRR1A, CROT, KIFC1, POLD4, CASP2, WHSC1, MPZL2, NAV1, RNF168, FOXM1, ZC3H11A, FAM3D, KCNK17, PLXNA2, SUOX, ANP32E, REST, NKX2.2, RBBP8, NSMCE4A, H19, ATP1A2, PLXNC1, NUP62, ACAA2, ADH1C, THYN1, COX7A2L, MAP1B or a combination thereof in a biological sample obtained from a subject; and

b) calculating an ADT resistance signature (ARS) score based on the level of expression of the plurality of biomarkers, wherein a higher ARS score for the subject compared to reference value ranges for a control subject indicates that the subject is resistant to ADT.

2 . The method of claim 1 , wherein the plurality of biomarker genes are selected from the group consisting of SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12 and NLRP13.

3 . The method of claim 1 , wherein the subject is undergoing ADT.

4 . The method of claim 1 , wherein the method is performed after treatment of the subject with ADT.

5 . The method of claim 1 , wherein the prostate cancer is adenocarcinoma.

6 . The method of claim 1 , wherein the prostate cancer is small cell prostate cancer.

7 . The method of claim 1 , wherein the prostate cancer is neuroendocrine prostate cancer.

8 . The method of claim 1 , wherein the method is performed after the subject undergoes radical prostatectomy.

9 . The method of claim 1 , wherein the prostate cancer is metastatic castration resistant prostate cancer.

10 . The method of claim 1 , wherein the biological sample is a biopsy.

11 . The method of claim 1 , wherein the biological sample is a tumor sample.

12 . The method of claim 1 , wherein the subject is a human being.

13 . The method of claim 1 , wherein measuring the level of expression comprises performing microarray analysis, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), a Northern blot, or serial analysis of gene expression (SAGE).

14 . A method for treating a subject for prostate cancer, the method comprising:

a) determining whether or not the subject is resistant to ADT according to the method of claim 1 ; and

b) administering ADT to the subject if the subject is not identified as resistant to ADT, or administering a cancer treatment other than ADT to the subject if the subject is identified as resistant to ADT.

15 . The method of claim 14 , wherein the subject identified as resistant to ADT is administered a cancer treatment comprising surgery, radiation therapy, chemotherapy, immunotherapy, biologic therapy, or any combination thereof.

16 . A kit comprising agents for measuring levels of expression of biomarker genes comprising SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12, NLRP13, MPP7, CFL1, DESI2, OR51E2, KCNMB1, DLGAP1, SPRR1A, CROT, KIFC1, POLD4, CASP2, WHSC1, MPZL2, NAV1, RNF168, FOXM1, ZC3H11A, FAM3D, KCNK17, PLXNA2, SUOX, ANP32E, REST, NKX2.2, RBBP8, NSMCE4A, H19, ATP1A2, PLXNC1, NUP62, ACAA2, ADH1C, THYN1, COX7A2L, MAP1B or a combination thereof.

17 . The kit of claim 16 , further comprising agents for measuring the levels of expression of one or more biomarker genes selected from the group consisting of SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12 and NLRP13.

18 . The kit of claim 16 , further comprising reagents for performing microarray analysis, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), a Northern blot, or serial analysis of gene expression (SAGE).

19 . The kit of claim 18 , wherein the kit comprises a microarray.

20 . The kit of claim 18 , wherein the kit comprises at least one set of PCR primers capable of amplifying a nucleic acid comprising a biomarker gene sequence.

21 . The kit of claim 18 , wherein the kit comprises at least one probe capable of hybridizing to a nucleic acid comprising a biomarker gene sequence or its complement.

22 . The kit of claim 16 , further comprising information, in electronic or paper form, comprising instructions on how to correlate the detected levels of each biomarker with resistance to ADT.

23 . The kit of claim 16 , further comprising one or more control reference samples.

24 . A method for predicting survival of a subject undergoing androgen deprivation therapy (ADT) for treatment of prostate cancer, the method comprising:

25 . The method of claim 24 , wherein the plurality of biomarker genes is selected from the group consisting of SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12 and NLRP13.

26 . The method of claim 24 , wherein the method is performed after treatment of the subject with ADT.

27 . The method of claim 24 , wherein the prostate cancer is adenocarcinoma.

28 . The method of claim 24 , wherein the prostate cancer is small cell prostate cancer.

29 . The method of claim 24 , wherein the prostate cancer is neuroendocrine prostate cancer.

30 . The method of claim 24 , wherein the method is performed after the subject undergoes radical prostatectomy.

31 . The method of claim 24 , wherein the prostate cancer is metastatic castration resistant prostate cancer.

32 . The method of claim 24 , wherein the biological sample is a biopsy.

33 . The method of claim 24 , wherein the biological sample is a tumor sample.

34 . The method of claim 24 , wherein the subject is a human being.

35 . The method of claim 24 , wherein measuring the level of expression comprises performing microarray analysis, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), a Northern blot, or a serial analysis of gene expression (SAGE).

36 . A computer implemented method for predicting resistance to androgen deprivation therapy (ADT) for a subject who has prostate cancer, the computer performing steps comprising:

a) receiving inputted subject data comprising values for the levels of expression of biomarker genes comprising SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12, NLRP13, MPP7, CFL1, DESI2, OR51E2, KCNMB1, DLGAP1, SPRR1A, CROT, KIFC1, POLD4, CASP2, WHSC1, MPZL2, NAV1, RNF168, FOXM1, ZC3H11A, FAM3D, KCNK17, PLXNA2, SUOX, ANP32E, REST, NKX2.2, RBBP8, NSMCE4A, H19, ATP1A2, PLXNC1, NUP62, ACAA2, ADH1C, THYN1, COX7A2L, MAP1B or a combination thereof in a biological sample comprising cancer cells from the subject;

b) analyzing the level of expression of each biomarker gene and comparing with respective reference value ranges for each biomarker gene;

c) calculating an ARS score for the subject based on the levels of expression of the biomarker genes, wherein a higher ARS score for the subject compared to reference value ranges for a control subject indicates that the subject is resistant to ADT; and

d) displaying information regarding whether or not the subject is resistant to ADT.

37 . The method of claim 36 , wherein the inputted subject data further comprises values for the levels of expression of one or more biomarker genes selected from the group consisting of SELE, B3GALTL, GABRB3, CLEC9A, PRKAG1, SLC35F2, CRYM, FBXO43, GALM, TMEM133, TFAP4, KCNH8, KIAA1210, LRRC18, PEX11A, CCDC151, MORN3, GLYATL1, EHHADH, LPGAT1, FAM134A, RLN1, DNAJC12, TXK, TM2D2, CDH26, RBPMS2, NUDT1, STMN1, EZH2, NAV2, SEMA3C, CCL16, HJURP, SOX14, NPR3, HEY2, SFTA3, C8orf4, PRTFDC1, HEPN1, ID2, ALDH2, LSM7, FAHD2A, TACC2, MSMB, KLK12 and NLRP13.

38 . The method of claim 36 , wherein the biological sample comprises a biopsy or tumor sample.

39 . A diagnostic system for performing the method of claim 36 comprising:

a) a storage component for storing data, wherein the storage component has instructions for predicting resistance to ADT according to the method of claim 36 stored therein;

b) a computer processor for processing data, wherein the computer processor is coupled to the storage component and configured to execute the instructions stored in the storage component in order to receive subject data and analyze subject data according to one or more algorithms; and

c) a display component for displaying information regarding the diagnosis of the subject.

40 . The diagnostic system of claim 39 , wherein the storage component includes instructions for calculating the ARS score of the subject.

41 . A diagnostic method for predicting resistance to androgen deprivation therapy (ADT) for a subject who has prostate cancer, the method comprising:

a) measuring the level of expression of a plurality of biomarker genes comprising DAND5, GABRB3, KLK12, NAV2, POGK, RIMS2, SNCAIP, TET1, TMEM176A, ELL2, ADAMTS14, CDKN2C, KCNMB2, MUC1, PLEKHH2, TNIK, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, POLD4, RRAS, SPATA13, TMEFF2, ARHGAP11A, ASB16, CASP2, FAM57B, FOXM1, GNAZ, AC084018.1, NAV1, RRM2, TFAP4, HEPN1, KIF1C, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, NUP210, CDH3, CREB3L1, SLC35F2, TRPV6, FAM134A, NSMCE4A or a combination thereof in a biological sample obtained from a subject; and

42 . The method of claim 41 , wherein the plurality of biomarker genes is selected from the group consisting of DAND5, GABRB3, RIMS2, SNCAIP, TMEM176A, KCNMB2, PLEKHH2, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, RRAS, SPATA13, TMEFF2, ARHGAP11A, GNAZ, AC084018.1, RRM2, TFAP4, HEPN1, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, CREB3L1, SLC35F2, FAM134A, and NSMCE4A.

43 . The method of claim 42 , wherein the plurality of biomarker genes further comprises one or more genes selected from the group consisting of KLK12, NAV2, POGK, TET1, ELL2, ADAMTS14, CDKN2C, MUC1, TNIK, POLD4, ASB16, CASP2, FAM57B, FOXM1, NAV1, KIF1C, NUP210, CDH3, and TRPV6.

44 . The method of claim 42 , wherein the plurality of biomarker genes comprises DAND5, GABRB3, KLK12, NAV2, POGK, RIMS2, SNCAIP, TET1, TMEM176A, ELL2, ADAMTS14, CDKN2C, KCNMB2, MUC1, PLEKHH2, TNIK, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, POLD4, RRAS, SPATA13, TMEFF2, ARHGAP11A, ASB16, CASP2, FAM57B, FOXM1, GNAZ, AC084018.1, NAV1, RRM2, TFAP4, HEPN1, KIF1C, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, NUP210, CDH3, CREB3L1, SLC35F2, TRPV6, FAM134A, NSMCE4A or a combination thereof.

45 . The method of claim 41 , wherein the subject is undergoing ADT.

46 . The method of claim 41 , wherein the method is performed after treatment of the subject with ADT.

47 . The method of claim 41 , wherein the prostate cancer is adenocarcinoma.

48 . The method of claim 41 , wherein the prostate cancer is small cell prostate cancer.

49 . The method of claim 41 , wherein the prostate cancer is neuroendocrine prostate cancer.

50 . The method of claim 41 , wherein the method is performed after the subject undergoes radical prostatectomy.

51 . The method of claim 41 , wherein the prostate cancer is metastatic castration resistant prostate cancer.

52 . The method of claim 41 , wherein the biological sample is a biopsy.

53 . The method of claim 41 , wherein the biological sample is a tumor sample.

54 . The method of claim 41 , wherein the subject is a human being.

55 . The method of claim 41 , wherein measuring the level of expression comprises performing microarray analysis, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), a Northern blot, or serial analysis of gene expression (SAGE).

56 . A method for treating a subject for prostate cancer, the method comprising:

c) determining whether or not the subject is resistant to ADT according to the method of claim 1 ; and

d) administering ADT to the subject if the subject is not identified as resistant to ADT, or administering a cancer treatment other than ADT to the subject if the subject is identified as resistant to ADT.

57 . The method of claim 56 , wherein the subject identified as resistant to ADT is administered a cancer treatment comprising surgery, radiation therapy, chemotherapy, immunotherapy, biologic therapy, or any combination thereof.

58 . A kit comprising agents for measuring levels of expression of biomarker genes comprising DAND5, GABRB3, RIMS2, SNCAIP, TMEM176A, KCNMB2, PLEKHH2, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, RRAS, SPATA13, TMEFF2, ARHGAP11A, GNAZ, AC084018.1, RRM2, TFAP4, HEPN1, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, CREB3L1, SLC35F2, FAM134A, NSMCE4A or a combination thereof.

59 . The kit of claim 58 , further comprising agents for measuring the levels of expression of one or more biomarker genes selected from the group consisting of KLK12, NAV2, POGK, TET1, ELL2, ADAMTS14, CDKN2C, MUC1, TNIK, POLD4, ASB16, CASP2, FAM57B, FOXM1, NAV1, KIF1C, NUP210, CDH3, and TRPV6.

60 . The kit of claim 59 , comprising agents for measuring the levels of expression of the biomarker genes DAND5, GABRB3, KLK12, NAV2, POGK, RIMS2, SNCAIP, TET1, TMEM176A, ELL2, ADAMTS14, CDKN2C, KCNMB2, MUC1, PLEKHH2, TNIK, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, POLD4, RRAS, SPATA13, TMEFF2, ARHGAP11A, ASB16, CASP2, FAM57B, FOXM1, GNAZ, AC084018.1, NAV1, RRM2, TFAP4, HEPN1, KIF1C, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, NUP210, CDH3, CREB3L1, SLC35F2, TRPV6, FAM134A, NSMCE4A or a combination thereof.

61 . The kit of claim 58 , further comprising reagents for performing microarray analysis, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), a Northern blot, or serial analysis of gene expression (SAGE).

62 . The kit of claim 61 , wherein the kit comprises a microarray.

63 . The kit of claim 61 , wherein the kit comprises at least one set of PCR primers capable of amplifying a nucleic acid comprising a biomarker gene sequence.

64 . The kit of claim 61 , wherein the kit comprises at least one probe capable of hybridizing to a nucleic acid comprising a biomarker gene sequence or its complement.

65 . The kit of claim 58 , further comprising information, in electronic or paper form, comprising instructions on how to correlate the detected levels of each biomarker with resistance to ADT.

66 . The kit of claim 58 , further comprising one or more control reference samples.

67 . A method for predicting survival of a subject undergoing androgen deprivation therapy (ADT) for treatment of prostate cancer, the method comprising:

c) measuring the level of expression of a plurality of biomarker genes comprising DAND5, GABRB3, KLK12, NAV2, POGK, RIMS2, SNCAIP, TET1, TMEM176A, ELL2, ADAMTS14, CDKN2C, KCNMB2, MUC1, PLEKHH2, TNIK, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, POLD4, RRAS, SPATA13, TMEFF2, ARHGAP11A, ASB16, CASP2, FAM57B, FOXM1, GNAZ, AC084018.1, NAV1, RRM2, TFAP4, HEPN1, KIF1C, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, NUP210, CDH3, CREB3L1, SLC35F2, TRPV6, FAM134A, NSMCE4A or a combination thereof in a biological sample obtained from a subject; and

d) calculating an ADT resistance signature (ARS) score based on the level of expression of the plurality of biomarkers, wherein a higher ARS score for the subject compared to reference value ranges for a control subject indicates that the subject will have a shorter period of metastasis-free survival compared to a subject who is not resistant to ADT.

68 . The method of claim 67 , wherein the plurality of biomarker genes is selected from the group consisting of DAND5, GABRB3, RIMS2, SNCAIP, TMEM176A, KCNMB2, PLEKHH2, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, RRAS, SPATA13, TMEFF2, ARHGAP11A, GNAZ, AC084018.1, RRM2, TFAP4, HEPN1, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, CREB3L1, SLC35F2, FAM134A, and NSMCE4A.

69 . The method of claim 68 , wherein the plurality of genes further comprises one or more genes selected from the group consisting of KLK12, NAV2, POGK, TET1, ELL2, ADAMTS14, CDKN2C, MUC1, TNIK, POLD4, ASB16, CASP2, FAM57B, FOXM1, NAV1, KIF1C, NUP210, CDH3, and TRPV6.

70 . The method of claim 69 , wherein the plurality of genes comprises DAND5, GABRB3, KLK12, NAV2, POGK, RIMS2, SNCAIP, TET1, TMEM176A, ELL2, ADAMTS14, CDKN2C, KCNMB2, MUC1, PLEKHH2, TNIK, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, POLD4, RRAS, SPATA13, TMEFF2, ARHGAP11A, ASB16, CASP2, FAM57B, FOXM1, GNAZ, AC084018.1, NAV1, RRM2, TFAP4, HEPN1, KIF1C, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, NUP210, CDH3, CREB3L1, SLC35F2, TRPV6, FAM134A, NSMCE4A or a combination thereof.

71 . The method of claim 67 , wherein the method is performed after treatment of the subject with ADT.

72 . The method of claim 67 , wherein the prostate cancer is adenocarcinoma.

73 . The method of claim 67 , wherein the prostate cancer is small cell prostate cancer.

74 . The method of claim 67 , wherein the prostate cancer is neuroendocrine prostate cancer.

75 . The method of claim 67 , wherein the method is performed after the subject undergoes radical prostatectomy.

76 . The method of claim 67 , wherein the prostate cancer is metastatic castration resistant prostate cancer.

77 . The method of claim 67 , wherein the biological sample is a biopsy.

78 . The method of claim 67 , wherein the biological sample is a tumor sample.

79 . The method of claim 67 , wherein the subject is a human being.

80 . The method of claim 67 , wherein measuring the level of expression comprises performing microarray analysis, polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR), a Northern blot, or a serial analysis of gene expression (SAGE).

81 . A computer implemented method for predicting resistance to androgen deprivation therapy (ADT) for a subject who has prostate cancer, the computer performing steps comprising:

e) receiving inputted subject data comprising values for the levels of expression of biomarker genes comprising DAND5, GABRB3, RIMS2, SNCAIP, TMEM176A, KCNMB2, PLEKHH2, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, RRAS, SPATA13, TMEFF2, ARHGAP11A, GNAZ, AC084018.1, RRM2, TFAP4, HEPN1, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, CREB3L1, SLC35F2, FAM134A, NSMCE4A or a combination thereof in a biological sample comprising cancer cells from the subject;

f) analyzing the level of expression of each biomarker gene and comparing with respective reference value ranges for each biomarker gene;

g) calculating an ARS score for the subject based on the levels of expression of the biomarker genes, wherein a higher ARS score for the subject compared to reference value ranges for a control subject indicates that the subject is resistant to ADT; and

h) displaying information regarding whether or not the subject is resistant to ADT.

82 . The method of claim 81 , wherein the inputted subject data further comprises values for the levels of expression of one or more biomarker genes selected from the group consisting of KLK12, NAV2, POGK, TET1, ELL2, ADAMTS14, CDKN2C, MUC1, TNIK, POLD4, ASB16, CASP2, FAM57B, FOXM1, NAV1, KIF1C, NUP210, CDH3, and TRPV6.

83 . The method of claim 82 , wherein the inputted subject data comprises values for the levels of expression of biomarker genes comprising DAND5, GABRB3, KLK12, NAV2, POGK, RIMS2, SNCAIP, TET1, TMEM176A, ELL2, ADAMTS14, CDKN2C, KCNMB2, MUC1, PLEKHH2, TNIK, AGTR1, BAG3, ClOorf81, C8orf4, CRISP2, GALM, GHR, POLD4, RRAS, SPATA13, TMEFF2, ARHGAP11A, ASB16, CASP2, FAM57B, FOXM1, GNAZ, AC084018.1, NAV1, RRM2, TFAP4, HEPN1, KIF1C, MPDU1, RLN1, SELE, WDR93, ATF5, HEY2, NUP210, CDH3, CREB3L1, SLC35F2, TRPV6, FAM134A, NSMCE4A or a combination thereof.

84 . The method of claim 81 , wherein the biological sample comprises a biopsy or tumor sample.

85 . A diagnostic system for performing the method of claim 81 comprising:

d) a storage component for storing data, wherein the storage component has instructions for predicting resistance to ADT according to the method of claim 81 stored therein;

e) a computer processor for processing data, wherein the computer processor is coupled to the storage component and configured to execute the instructions stored in the storage component in order to receive subject data and analyze subject data according to one or more algorithms; and

f) a display component for displaying information regarding the diagnosis of the subject.

86 . The diagnostic system of claim 85 , wherein the storage component includes instructions for calculating the ARS score of the subject.

Assignments (8)

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 22, 2023

From: VERACYTE SD, INC.

To: VERACYTE, INC.

Reel/Frame 065651/0354 →

CHANGE OF NAME Recorded Nov 21, 2023

From: DECIPHER BIOSCIENCES, INC.

To: VERACYTE SD, INC.

Reel/Frame 065659/0780 →

RELEASE OF SECURITY INTEREST Recorded Mar 15, 2021