US 10,892,038 B2
Method to use gene expression to determine likelihood of clinical outcome of renal cancer
Wayne Cowens; Steven Shak, Hillsborough, CA (US); Audrey Goddard, San Francisco, CA (US); Dejan Knezevic, Palo Alto, CA (US); Joffre Baker, Montara, CA (US); Michael C. Kiefer, Walnut Creek, CA (US); Tara Maddala, Sunnyvale, CA (US); and Frederick L. Baehner, San Francisco, CA (US)
Assigned to Genomic Health, Inc., Redwood City, CA (US)
Filed by GENOMIC HEALTH, INC., Redwood City, CA (US)
Filed on Dec. 5, 2016, as Appl. No. 15/368,979.
Application 15/368,979 is a continuation of application No. 12/987,023, filed on Jan. 7, 2011, granted, now 9,551,034.
Claims priority of provisional application 61/294,038, filed on Jan. 11, 2010.
Claims priority of provisional application 61/346,230, filed on May 19, 2010.
Prior Publication US 2017/0121780 A1, May 4, 2017
Int. Cl. G01N 33/574 (2006.01); G16B 99/00 (2019.01); G06N 7/00 (2006.01)
CPC G16B 99/00 (2019.02) [G01N 33/57438 (2013.01); G06N 7/005 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/158 (2013.01)] 22 Claims
 
1. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, comprising:
measuring a level of an RNA transcript, in a renal tumor sample from the patient, of a panel of genes consisting of:
(a) a set of genes consisting of one or more genes selected from: YBX1, XIAP, WWOX, VWF, VEGFA, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TYMS, TUSC4, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNFSF12, TNFSF10, TNFRSF11B, TNFRSF10D, TNFRSF10B, TNFAIP6, TMEM47, TM2M27, TLR3, TIMP3, TIMP2, THBS1, TGFBR2, IGF1R, IF127, ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSD11B2, HPN, HPCAL1, HMGB1, HLA-DPB1, HIF1AN, HDAC1, HAVCR1, HADH, GZMA, GSTP1, GSTM3, GSTM1, GRB7, GPX3, GJA1, GFRA1, GCLC, GBP2, GATM, GATA3, FOS, TGFBR1, TGFB2, TGFA, TEK, TCF4, TAP1, TAGLN, TACSTD2, SUCLG1, STK11, STAT5B, STAT5A, STATS, SPRY1, SPARCL1, SPARC, SOD1, SNRK, SNAI1, SMAD4, SMAD2, SLC34A1, SLC22A6, SKIL, SHANKS, SGK1, SFRP1, SEMA3F, SELENBP1, SDPR, SDHA, SCNN1A, FOLR1, FLT4, FLT3LG, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAS, FABP1, ESRRG, ERG, ERCC1, ERBB3, ERBB2, EPHB4, EPHA2, EPAS1, ENPP2, ENPEP, ENG, EMP1, EMCN, ELTD1, EIF2C1, SCN4B, RPTOR, RPS6KB1, RPS6KA1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RGS5, RERGL, RELA, RB1, RASSF1, BARB, RALBP1, RAF1, PTPRG, PTPRB, PTN, PTK2, PTH1R, PTEN, PSMB9, PSMB8, PRSS8, PRPS2, PRKCH, PPP2CA, EGR1, EGLN3, EGFR, EFNB2, EFNB1, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPYS, DPEP1, DLL4, DLC1, DKFZP564O0823, DICER1, DIAPH1, DIABLO, DHPS, DET1, DEFB1, DDC, DCXR, DAPK1, CYR61, CYP3A4, CXCL9, CXCL12, CX3CR1, CX3CL1, PPARG, PPAP2B, PLG, PLAT, PLA2G4C, PIK3CA, PIK3C2B, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFD, PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, NRG1, NPR1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2, NOL3, NFX1, CUL1, CUBN, CTSS, CTSH, CTNNB1, CTNNA1, CTGF, CSF1R, CSF1, CRADD, COL4A2, COL18A1, CLU, CLDN7, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1B, CDKN1A, CDH6, CDH5, CDH16, CDH13, CD4, CD36, CD34, CCR7, CCR4, CCND1, CCL4, CCL2, CAT, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MVP, MUC1, MTOR, MSH3, MSH2, MLST8, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAPK3, MAPK1, MAP4, MAP2K3, MAP2K1, MAL2, MAL, LYZ, LTF, LRP2, LMO2, LDB2, LDB1, LAMA4, KRT7, CASP6, CASP10, CALD1, CA9, CA2, C7, C2 orf40, C13orf15, BUB3, BTRC, BIRC2, BIN1, BGN, BCL2L12, BCL2L1, BCL2, BBC3, BAG1, BAD, ATP6V1B1, ASS1, ARRB1, ARHGDIB, AQP1, APOLD1, APC, ANXA4, ANXA1, ANTXR1, ANGPTL4, ANGPTL3, ANGPT1, ALDOB, KRAS, KL, KITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, JAG1, ITGB1, ITGA7, ITGA6, ITGA4, ITGA3, IQGAP2, INSR, IMPS, IL6ST, IL15, IGFBP6, IGFBP3, IGFBP2, ALDH6A1, ALDH4A1, AKT3, AKT2, AKT1, AIF1, AHR, AGTR1, ADH1B, ADFP, ADD1, ADAMTS5, ADAMTS1, ACE2, ACADSB, ABCG2, ABCC4, ABCC3, ABCC1, ABCB1, ABAT, AAMP, and A2M;
(b) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, VCAN, UBE2T, TPX2, TOP2A, TK1, TIMP1, TGFBI, SQSTM1, SPP1, SPHK1, SLC7A5, SLC2A1, SLC16A3, SLC13A3, SHC1, SFN, SERPINA5, SEMA3C, SAA2, S100A1, RRM2, RPLP1, PTTG1, PTGS2, PLAUR, PF4, PCSK6, MYBL2, MT1X, MMP9, LGALS1, LAMBS, LAMB1, L1CAM, IL8, IL6, ICAM1, HIST1H1D, FN1, F3, F2, ESPL1, EPHB2, EPHB1, ENO2, EIF4EBP1, CXCR4, CXCL1, CTSB, CRP, CP, COL7A1, COL1A1, CHEK1, CENPF, CD82, CD44_s, CCNE1, CCNB1, CCL20, CA12, C3, BUB1, MMP7, MMP14, MKI67, MGST1, MDK, LOX, LMNB1, LIMK1, BIRC5, BIRC3, BCL2A1, AURKA, ANXA2, ALOX5, ADAM8, and ABCC2;
(c) a set of genes consisting of one or more genes selected from: ACE2, ADD1, ALDOB, ANGPTL3, APOLD1, AQP1, NUDT6, CASP10, CAV2, CCL4, CCL5, CCR2, CCR4, CCR7, CD4, CD8A, CEACAM1, CFLAR, CTSS, CX3CL1, CXCL10, CXCL9, CXCR6, DAPK1, DDC, DLC1, C2 orf40, EDNRB, EMCN, EPAS1, FAS, FH, GATA3, GZMA, HLA-DPB1, HSPG2, ICAM2, ICAM3, ID1, IGF1R, IL15, IQGAP2, KLRK1, LDB2, LRP2, LTF, MAP4, ABCC1, NOS3, PIK3C2B, PLA2G4C, PPAP2B, PRCC, PRKCB, PRKCH, PRSS8, PSMB9, PTPRB, RGS5, SDPR, SELE, SGK1, SHANKS, SNRK, TEK, TGFBR2, TIMP3, TMEM27, TSPAN7, UBB, and WWOX; and
(d) a set of consisting of one or more genes selected from: BIRC2, BUB1, CCNB1, ENO2, ITGB1, ITGB5, LAMB1, MMP14, MMP9, PSMA7, RUNX1, SPHK1, SPP1, SQSTM1, TPX2, TUBBA2, and VCAN;
wherein the gene(s) of the sets do not overlap, and wherein one or more of AAMP, RPS23, SDHA, UBB, and RPLP1 is a member of the panel.