| CPC C12Q 1/6886 (2013.01) [C12Q 2600/112 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/158 (2013.01)] | 4 Claims |
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1. A method of predicting prostate cancer progression, comprising:
a) determining the expression status of at least 50 genes selected from the group consisting of: TGM4, RLN1, ORM1, OLFM4, OR51E2, SERPINB11, CRISP3, TDRD1, SLC14A1, IGJ, ERG, GDEP, TMEFF2, CST1, LTF, AMACR, SERPINA3, NEFH, ACSM1, OR51E1, MT1G, ANKRD36B, LOC100510059, PLA2G2A, TARP, REXO1L1, ANPEP, HLA-DRB5, PLA2G7, NCAPD3, OR51F2, SPINK1, RCN1, CP, SMU1, ACTC1, AGR2, SLC26A4, IGKC, MYBPC1, NPY, PI15, SLC22A3, PIGR, MME, RBPMS, HLA-DRB1, FOLH1, LUZP2, MSMB, GSTT1, MMP7, ODZ1, ACTB, SPON2, SLC38A11, FOS, OR51T1, HLA-DMB, KRT15, ITGA8, CXADR, LYZ, CEACAM20, C8orf4, DPP4, PGC, C15orf21, CHORDC1, LRRN1, MT1M, EPHA6, PDE11A, TMSB15A, LYPLA1, FOSB, F5, C15orf48, MIPEP, HSD17B6, SLPI, CD38, MMP23B, OR51A7, CFB, CCL2, POTEM, TPMT, FAM3B, FLRT3, C7, NTN4, FAM36A, CNTNAP2, SC4MOL, CH17-189H20.1, TRGC2, RAP1B, SLC4A4, LCE2D, EGR1, MT1L, SCUBE2, FAM55D, PDK4, CXCL13, CACNA1D, GPR160, CPM, PTGS2, TSPAN8, BMP5, GOLGA8A, OR4N2, FAM135A, DYNLL1, DSC3, C4orf3, HIST1H2BK, LCN2, STEAP4, RPS27L, TRPM8, ID2, LUM, EDNRB, PGM5, SFRP4, STEAP1, FADS2, CXCL11, CWH43, SNRPN, GPR110, THBS1, APOD, HPGD, LEPREL1, LCE1D, GSTM5, SLC30A4, SEMA3D, CACNA2D1, GPR116, C7orf63, FAM198B, SCD, NR4A2, ARG2, ZNF385B, RGS1, DNAH5, NPR3, RAB3B, CHRDL1, ZNF208, MBOAT2, ATF3, ST6GAL1, GDF15, ANXA1, FOLH1, C4B, ELOVL2, GSTM1, GLIPR1, C3, MYO6, ORM2, RAET1L, PCDHB3, C1orf150, ALOX15B, LSAMP, SLC15A2, PCP4, MCCC2, GCNT1, C5orf23, SCGB1D2, CXCL2, AFF3, ATP8A2, PRIM2, ADAMTSL1, NELL2, RPS4Y1, CD24, GOLGA6L9, ZFP36, TRIB1, BNIP3, KL, PDE5A, DCN, LDHB, PCDHB5, ACADL, ZNF99, CPNE4, CCDC144B, SLC26A2, CYP1B1, SELE, CLDN1, KRT13, SFRP2, SLC25A33, HSD17B11, HSD17B13, UGT2B4, CTGF, SCIN, C10orf81, CYR61, PRUNE2, IFI6, MYH11, PPP1R3C, KCNH8, ZNF615, ERV3, F3, TTN, LYRM5, FMOD, NEXN, IL28A, FHL1, CXCL10, SPOCK1, GSTP1, OAT, HIST2H2BF, ACSM3, GLB1L3, SLC5A1, OR4N4, MAOB, BZW1, GENSCAN00000007309, IFI44L, KRT5, SCN7A, GOLM1, HIST4H4, IL7R, CSGALNACT1, A2M, LRRC9, ARHGEF38, ACSL5, SGK1, TMEM45B, AHNAK2, NEDD8, GREB1, UBQLN4, SDHC, TCEAL2, SLC18A2, HIST1H2BE, RARRES1, PLN, OGN, GPR110, CLGN, NIPAL3, ACTG2, RCAN3, KLK11, HMGCS2, EML5, EDIL3, PIGH, GLYATL1, ATP1B1, GJA1, PLA1A, MPPED2, AMD1, EMP1, PRR16, CNN1, GHR, ALDH1A1, TRIM29, IFNA17, TAS2R4, SEPP1, GREM1, RASD1, C1S, CLSTN2, DMXL1, HIST1H2BC, NRG4, ARL17A, GRPR, PART1, CYP3A5, KCNC2, SERPINE1, SLC6A14, EIF4A1, MYOF, PHOSPHO2, GCNT2, AOX1, CCDC80, ATP2B4, UGDH, GSTM2, MEIS2, RGS2, PRKG2, FIBIN, FDXACB1, SOD2, SEPT7, PTPRC, GABRP, CBWD3, TOR1AIP2, CXCR4, OR51L1, SLC12A2, AGAP11, SLC27A2, AZGP1, VCAN, ERAP2, KRT17, SLC2A12, CCL4, RPF2, SLC45A3, SEC11C, IFIT1, PAK1IP1, HIST1H3C, ERRFI1, ADAMTS1, TRIM36, FLNA, CCND2, IFIT3, FN1, PRY, HSPB8, CD177, TP63, IFI44, COL12A1, EDNRA, PCDHB2, HLA-DRA, TUBA3E, ASPN, FAM127A, DMD, DHRS7, ANO7, MEIS1, TSPAN1, CNTN1, TRIM22, GSTA2, SORBS1, GPR81, CSRP1, C3orf14, FGFR2, SNAI2, CALCRL, MON1B, PVRL3, VGLL3, SULF1, LIFR, SH3RF1, C12orf75, GNPTAB, CALM2, KLF6, C7orf58, RDH11, NR4A1, RWDD4, ABCC4, ZNF91, GABRE, SLC16A1, DEGS1, CLDN8, HAS2, ODC1, REEP3, LYRM4, PPFIA2, PGM3, ZDHHC8P1, C6orf72, HIST1H2BD, TES, PDE8B, DNAJB4, RGS5, EPHA3, COX7A2, MT1H, HIST2H2BE, TGFB3, VEGFA, CRISPLD2, TFF1, LOC100128816, SYT1, CPE, TRPC4, RAB27A, CD69, RPL17, PSCA, ATRNL1, MYOCD, MS4A8B, TNS1, BAMBI, IGF1, RALGAPA1, S100A10, PMS2CL, MMP2, SLC8A1, OAS2, ARRDC3, AMY2B, SPARCL1, IQGAP2, ACAD8, LPAR3, HIGD2A, NUCB2, HLA-DPA1, SLITRK6, TPM2, REPS2, EAF2, CAV1, PRUNE2, TMEM178, MFAP4, SYNM, EFEMP1, RND3, SCNN1A, B3GNT5, LMOD1, UBC, LMO3, LOX, NFIL3, C11orf92, C11orf48, BCAP29, EPCAM, PTGDS, A5B5, TUBA1B, SERHL, ITGA5, SPARC, LOC286161, NAALADL2, TMPRSS2, SERPINF1, EPHA7, SDAD1, SOX14, RPL35, HSPA1B, MSN, MTRF1L, PTN, CAMKK2, RBM7, OR52H1, C1R, CHRNA2, MRPL41, PROM1, LPAR6, SAMHD1, SCNN1G, DNAJC10, MOXD1, HIST1H2BG, ID1, and SEMA3C in a sample obtained from a patient to provide a patient expression profile, wherein the expression level of the at least 50 genes selected from the group consisting of TGM4, RLN1, ORM1, OLFM4, OR51E2, SERPINB11, CRISP3, TDRD1, SLC14A1, IGJ, ERG, GDEP, TMEFF2, CST1, LTF, AMACR, SERPINA3, NEFH, ACSM1, OR51E1, MT1G, ANKRD36B, LOC100510059, PLA2G2A, TARP, REXO1L1, ANPEP, HLA-DRB5, PLA2G7, NCAPD3, OR51F2, SPINK1, RCN1, CP, SMU1, ACTC1, AGR2, SLC26A4, IGKC, MYBPC1, NPY, PI15, SLC22A3, PIGR, MME, RBPMS, HLA-DRB1, FOLH1, LUZP2, MSMB, GSTT1, MMP7, ODZ1, ACTB, SPON2, SLC38A11, FOS, OR51T1, HLA-DMB, KRT15, ITGA8, CXADR, LYZ, CEACAM20, C8orf4, DPP4, PGC, C15orf21, CHORDC1, LRRN1, MT1M, EPHA6, PDE11A, TMSB15A, LYPLA1, FOSB, F5, C15orf48, MIPEP, HSD17B6, SLPI, CD38, MMP23B, OR51A7, CFB, CCL2, POTEM, TPMT, FAM3B, FLRT3, C7, NTN4, FAM36A, CNTNAP2, SC4MOL, CH17-189H20.1, TRGC2, RAP1B, SLC4A4, LCE2D, EGR1, MT1L, SCUBE2, FAM55D, PDK4, CXCL13, CACNA1D, GPR160, CPM, PTGS2, TSPAN8, BMP5, GOLGA8A, OR4N2, FAM135A, DYNLL1, DSC3, C4orf3, HIST1H2BK, LCN2, STEAP4, RPS27L, TRPM8, ID2, LUM, EDNRB, PGM5, SFRP4, STEAP1, FADS2, CXCL11, CWH43, SNRPN, GPR110, THBS1, APOD, HPGD, LEPREL1, LCE1D, GSTM5, SLC30A4, SEMA3D, CACNA2D1, GPR116, C7orf63, FAM198B, SCD, NR4A2, ARG2, ZNF385B, RGS1, DNAH5, NPR3, RAB3B, CHRDL1, ZNF208, MBOAT2, ATF3, ST6GAL1, GDF15, ANXA1, FOLH1, C4B, ELOVL2, GSTM1, GLIPR1, C3, MYO6, ORM2, RAET1L, PCDHB3, C1orf150, ALOX15B, LSAMP, SLC15A2, PCP4, MCCC2, GCNT1, C5orf23, SCGB1D2, CXCL2, AFF3, ATP8A2, PRIM2, ADAMTSL1, NELL2, RPS4Y1, CD24, GOLGA6L9, ZFP36, TRIB1, BNIP3, KL, PDE5A, DCN, LDHB, PCDHB5, ACADL, ZNF99, CPNE4, CCDC144B, SLC26A2, CYP1B1, SELE, CLDN1, KRT13, SFRP2, SLC25A33, HSD17B11, HSD17B13, UGT2B4, CTGF, SCIN, C10orf81, CYR61, PRUNE2, IFI6, MYH11, PPP1R3C, KCNH8, ZNF615, ERV3, F3, TTN, LYRM5, FMOD, NEXN, IL28A, FHL1, CXCL10, SPOCK1, GSTP1, OAT, HIST2H2BF, ACSM3, GLB1L3, SLC5A1, OR4N4, MAOB, BZW1, GENSCAN00000007309, IFI44L, KRT5, SCN7A, GOLM1, HIST4H4, IL7R, CSGALNACT1, A2M, LRRC9, ARHGEF38, ACSL5, SGK1, TMEM45B, AHNAK2, NEDD8, GREB1, UBQLN4, SDHC, TCEAL2, SLC18A2, HIST1H2BE, RARRES1, PLN, OGN, GPR110, CLGN, NIPAL3, ACTG2, RCAN3, KLK11, HMGCS2, EML5, EDIL3, PIGH, GLYATL1, ATP1B1, GJA1, PLA1A, MPPED2, AMD1, EMP1, PRR16, CNN1, GHR, ALDH1A1, TRIM29, IFNA17, TAS2R4, SEPP1, GREM1, RASD1, C1S, CLSTN2, DMXL1, HIST1H2BC, NRG4, ARL17A, GRPR, PART1, CYP3A5, KCNC2, SERPINE1, SLC6A14, EIF4A1, MYOF, PHOSPHO2, GCNT2, AOX1, CCDC80, ATP2B4, UGDH, GSTM2, MEIS2, RGS2, PRKG2, FIBIN, FDXACB1, SOD2, SEPT7, PTPRC, GABRP, CBWD3, TOR1AIP2, CXCR4, OR51L1, SLC12A2, AGAP11, SLC27A2, AZGP1, VCAN, ERAP2, KRT17, SLC2A12, CCL4, RPF2, SLC45A3, SEC11C, IFIT1, PAK1IP1, HIST1H3C, ERRFI1, ADAMTS1, TRIM36, FLNA, CCND2, IFIT3, FN1, PRY, HSPB8, CD177, TP63, IFI44, COL12A1, EDNRA, PCDHB2, HLA-DRA, TUBA3E, ASPN, FAM127A, DMD, DHRS7, ANO7, MEIS1, TSPAN1, CNTN1, TRIM22, GSTA2, SORBS1, GPR81, CSRP1, C3orf14, FGFR2, SNAI2, CALCRL, MON1B, PVRL3, VGLL3, SULF1, LIFR, SH3RF1, C12orf75, GNPTAB, CALM2, KLF6, C7orf58, RDH11, NR4A1, RWDD4, ABCC4, ZNF91, GABRE, SLC16A1, DEGS1, CLDN8, HAS2, ODC1, REEP3, LYRM4, PPFIA2, PGM3, ZDHHC8P1, C6orf72, HIST1H2BD, TES, PDE8B, DNAJB4, RGS5, EPHA3, COX7A2, MT1H, HIST2H2BE, TGFB3, VEGFA, CRISPLD2, TFF1, LOC100128816, SYT1, CPE, TRPC4, RAB27A, CD69, RPL17, PSCA, ATRNL1, MYOCD, MS4A8B, TNS1, BAMBI, IGF1, RALGAPA1, S100A10, PMS2CL, MMP2, SLC8A1, OAS2, ARRDC3, AMY2B, SPARCL1, IQGAP2, ACAD8, LPAR3, HIGD2A, NUCB2, HLA-DPA1, SLITRK6, TPM2, REPS2, EAF2, CAV1, PRUNE2, TMEM178, MFAP4, SYNM, EFEMP1, RND3, SCNN1A, B3GNT5, LMOD1, UBC, LMO3, LOX, NFIL3, C11orf92, C11orf48, BCAP29, EPCAM, PTGDS, ASB5, TUBA1B, SERHL, ITGA5, SPARC, LOC286161, NAALADL2, TMPRSS2, SERPINF1, EPHA7, SDAD1, SOX14, RPL35, HSPA1B, MSN, MTRF1L, PTN, CAMKK2, RBM7, OR52H1, C1R, CHRNA2, MRPL41, PROM1, LPAR6, SAMHD1, SCNN1G, DNAJC10, MOXD1, HIST1H2BG, ID1, and SEMA3C are known to vary across prostate cancers;
b) conducting a Latent Process Decomposition (LPD) analysis on the patient expression profile and a reference dataset for the same at least 50 genes selected from the group consisting of TGM4, RLN1, ORM1, OLFM4, OR51E2, SERPINB11, CRISP3, TDRD1, SLC14A1, IGJ, ERG, GDEP, TMEFF2, CST1, LTF, AMACR, SERPINA3, NEFH, ACSM1, OR51E1, MT1G, ANKRD36B, LOC100510059, PLA2G2A, TARP, REXO1L1, ANPEP, HLA-DRB5, PLA2G7, NCAPD3, OR51F2, SPINK1, RCN1, CP, SMU1, ACTC1, AGR2, SLC26A4, IGKC, MYBPC1, NPY, PI15, SLC22A3, PIGR, MME, RBPMS, HLA-DRB1, FOLH1, LUZP2, MSMB, GSTT1, MMP7, ODZ1, ACTB, SPON2, SLC38A11, FOS, OR51T1, HLA-DMB, KRT15, ITGA8, CXADR, LYZ, CEACAM20, C8orf4, DPP4, PGC, C15orf21, CHORDC1, LRRN1, MT1M, EPHA6, PDE11A, TMSB15A, LYPLA1, FOSB, F5, C15orf48, MIPEP, HSD17B6, SLPI, CD38, MMP23B, OR51A7, CFB, CCL2, POTEM, TPMT, FAM3B, FLRT3, C7, NTN4, FAM36A, CNTNAP2, SC4MOL, CH17-189H20.1, TRGC2, RAP1B, SLC4A4, LCE2D, EGR1, MT1L, SCUBE2, FAM55D, PDK4, CXCL13, CACNA1D, GPR160, CPM, PTGS2, TSPAN8, BMP5, GOLGA8A, OR4N2, FAM135A, DYNLL1, DSC3, C4orf3, HIST1H2BK, LCN2, STEAP4, RPS27L, TRPM8, ID2, LUM, EDNRB, PGM5, SFRP4, STEAP1, FADS2, CXCL11, CWH43, SNRPN, GPR110, THBS1, APOD, HPGD, LEPREL1, LCE1D, GSTM5, SLC30A4, SEMA3D, CACNA2D1, GPR116, C7orf63, FAM198B, SCD, NR4A2, ARG2, ZNF385B, RGS1, DNAH5, NPR3, RAB3B, CHRDL1, ZNF208, MBOAT2, ATF3, ST6GAL1, GDF15, ANXA1, FOLH1, C4B, ELOVL2, GSTM1, GLIPR1, C3, MYO6, ORM2, RAET1L, PCDHB3, C1orf150, ALOX15B, LSAMP, SLC15A2, PCP4, MCCC2, GCNT1, C5orf23, SCGB1D2, CXCL2, AFF3, ATP8A2, PRIM2, ADAMTSL1, NELL2, RPS4Y1, CD24, GOLGA6L9, ZFP36, TRIB1, BNIP3, KL, PDE5A, DCN, LDHB, PCDHB5, ACADL, ZNF99, CPNE4, CCDC144B, SLC26A2, CYP1B1, SELE, CLDN1, KRT13, SFRP2, SLC25A33, HSD17B11, HSD17B13, UGT2B4, CTGF, SCIN, C10orf81, CYR61, PRUNE2, IFI6, MYH11, PPP1R3C, KCNH8, ZNF615, ERV3, F3, TTN, LYRM5, FMOD, NEXN, IL28A, FHL1, CXCL10, SPOCK1, GSTP1, OAT, HIST2H2BF, ACSM3, GLB1L3, SLC5A1, OR4N4, MAOB, BZW1, GENSCAN00000007309, IFI44L, KRT5, SCN7A, GOLM1, HIST4H4, IL7R, CSGALNACT1, A2M, LRRC9, ARHGEF38, ACSL5, SGK1, TMEM45B, AHNAK2, NEDD8, GREB1, UBQLN4, SDHC, TCEAL2, SLC18A2, HIST1H2BE, RARRES1, PLN, OGN, GPR110, CLGN, NIPAL3, ACTG2, RCAN3, KLK11, HMGCS2, EML5, EDIL3, PIGH, GLYATL1, ATP1B1, GJA1, PLA1A, MPPED2, AMD1, EMP1, PRR16, CNN1, GHR, ALDH1A1, TRIM29, IFNA17, TAS2R4, SEPP1, GREM1, RASD1, C1S, CLSTN2, DMXL1, HIST1H2BC, NRG4, ARL17A, GRPR, PART1, CYP3A5, KCNC2, SERPINE1, SLC6A14, EIF4A1, MYOF, PHOSPHO2, GCNT2, AOX1, CCDC80, ATP2B4, UGDH, GSTM2, MEIS2, RGS2, PRKG2, FIBIN, FDXACB1, SOD2, SEPT7, PTPRC, GABRP, CBWD3, TOR1AIP2, CXCR4, OR51L1, SLC12A2, AGAP11, SLC27A2, AZGP1, VCAN, ERAP2, KRT17, SLC2A12, CCL4, RPF2, SLC45A3, SEC11C, IFIT1, PAK1IP1, HIST1H3C, ERRFI1, ADAMTS1, TRIM36, FLNA, CCND2, IFIT3, FN1, PRY, HSPB8, CD177, TP63, IFI44, COL12A1, EDNRA, PCDHB2, HLA-DRA, TUBA3E, ASPN, FAM127A, DMD, DHRS7, ANO7, MEIS1, TSPAN1, CNTN1, TRIM22, GSTA2, SORBS1, GPR81, CSRP1, C3orf14, FGFR2, SNAI2, CALCRL, MON1B, PVRL3, VGLL3, SULF1, LIFR, SH3RF1, C12orf75, GNPTAB, CALM2, KLF6, C7orf58, RDH11, NR4A1, RWDD4, ABCC4, ZNF91, GABRE, SLC16A1, DEGS1, CLDN8, HAS2, ODC1, REEP3, LYRM4, PPFIA2, PGM3, ZDHHC8P1, C6orf72, HIST1H2BD, TES, PDE8B, DNAJB4, RGS5, EPHA3, COX7A2, MT1H, HIST2H2BE, TGFB3, VEGFA, CRISPLD2, TFF1, LOC100128816, SYT1, CPE, TRPC4, RAB27A, CD69, RPL17, PSCA, ATRNL1, MYOCD, MS4A8B, TNS1, BAMBI, IGF1, RALGAPA1, S100A10, PMS2CL, MMP2, SLC8A1, OAS2, ARRDC3, AMY2B, SPARCL1, IQGAP2, ACAD8, LPAR3, HIGD2A, NUCB2, HLA-DPA1, SLITRK6, TPM2, REPS2, EAF2, CAV1, PRUNE2, TMEM178, MFAP4, SYNM, EFEMP1, RND3, SCNN1A, B3GNT5, LMOD1, UBC, LMO3, LOX, NFIL3, C11orf92, C11orf48, BCAP29, EPCAM, PTGDS, ASB5, TUBA1B, SERHL, ITGA5, SPARC, LOC286161, NAALADL2, TMPRSS2, SERPINF1, EPHA7, SDAD1, SOX14, RPL35, HSPA1B, MSN, MTRF1L, PTN, CAMKK2, RBM7, OR52H1, C1R, CHRNA2, MRPL41, PROM1, LPAR6, SAMHD1, SCNN1G, DNAJC10, MOXD1, HIST1H2BG, ID1, and SEMA3C from different patients;
c) optionally repeating the analysis step b) multiple times; and
d) predicting prostate cancer progression,
wherein:
the LPD analysis organises individual patient expression profiles into groups; and
for each expression profile, the LPD analysis determines a continuous contribution (pi) of each group to the overall expression profile for each patient expression profile with DESNT processes contributing to poor prognosis and non-DESNT contributing to non-poor prognosis.
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