Methods for identifying genes which predict disease outcome for patients with colon cancer

A method for determining the prognosis of a subject having colon cancer, said method comprising:

• obtaining a biological sample from the subject;
• detecting the expression level of at least five genes selected from a group of 101 genes informative of colon cancer prognosis consisting of NARS, WDR1, WARS, CCT4, ATP5B, SORD, UBE2L6, PSME2, AIP, RRM2, LRRC41, CCT2, TAF9, HDAC5, SVIL, CCNB2, DBN1, PBX2, RFC5, IDE, MAD2L1, PSMA4, NDUFC1, IVD, PPIH, NEO1, CXCL10, FXN, GABBR1, ARHGAP8, LOC553158, HOXA4, COMMD4, DFFB, KLF12, GLMN, CASP7, PIR, ATP5G3, ACTN1, DDOST, TAPBP, RGL2, CYB561, TUSC3, C3orf63, GRB10, NR2F1, WDR68, CXCL2, CNPY2, CASP1, INDO, PFKM, CXCL11, MCAM, MAP2K5, MRPS11, NOLC1, CD59, CAMSAP1L1, SHANK2, KLC1, EMP1, C1orf95, GMDS, RPLP0, RPLP0-like, PDLIM4, PAM, TM4SF1, BEX4, ADORA1, FAM48A, ITM2B, PREB, CMPK1, LAP3, FAM82C, AACS, RP5-1077B9.4, NUP37, RHBDF1, PBK, TIPIN, TMEM204, ALG6, NPR3, SCD5, FLJ13236, GPATCH4, GREM2, RPL22, KLHL3, C15orf44, USP3, TNS1, ZBTB20, RTN2, FLJ10357, and CALML4, in the biological sample;
• comparing the detected expression level of the at least five genes from the biological sample with expression levels of the corresponding at least five genes when associated with a good disease prognosis expression profile and when associated with a bad disease prognosis expression profile;
• and
• determining the prognosis of the subject having colon cancer based on said comparing.

A method of identifying an agent that improves the prognosis of a subject having colon cancer, said method comprising:

• administering an agent to the subject having colon cancer;
• obtaining a first biological sample from the subject before said administering and a second biological sample from the subject after said administering;
• detecting the expression level of at least five genes selected from a group of 176 genes informative of colon cancer prognosis consisting of SLC25A3, WDR1, WARS, DAZAP2, TEGT, H2AFZ, SF3B1, ERP29, PSMA5, ATP5B, DHX15, SOX4, DDX23, SORD, LOC100131861, SAMM50, SFPQ, NISCH, CYB5B, UBE2L6, MCM5, TMEM106C, AIP, SMG7, AKR1A1, LRRC41, CCT2, EGFR, LANCL1, ASNA1, ARL2BP, UQCRH, N4BP2L2, CFB, ACSL4, MCRS1, TNFSF10, TES, ZMYM2, SERPINA1, KIF13B, TLN1, CCNA2, NDUFC1, COX5A, STK3, PIGR, SYNGR1, IFT88, HOXB7, GCHFR, ARL4A, ITGAE, PRDM2, C8orf70, PEBP1, PDGFA, LAMP3, SMURF2, GSR, MMP3, ZC3H7B, GRP, GALNS, COMMD4, PGDS, ZNF430, IL15RA, OGT, ZNF117, PSMD9, XPO7, YBX1, SRP72, UQCRFS1, UCP2, NUMB, GHITM, SLC39A8, NAB1, TNFRSF10B, GRB10, WDR68, OSBPL3, CNPY2, CXCL11, SSNA1, RECQL, VPS41, FDFT1, AP3D1, CASP1, PTHLH, C1orf144, UNC84A, MTUS1, TMEM87A, KIAA0746, SERINC2, SCAMP1, DOCK9, FRYL, R3HCC1, MAPKAPK5, LRRC47, PAM, COBL, TNIK, CDR2L, USP12, TMCC1, MFHAS1, METTL3, KLC1, MYRIP, RPLP0, RPLP0-like, CLN5, C19orf36, NAT1, CDC42BPA, SGCD, GSTA1, AL359599*, ZMYM5, GRHPR, RYK, CYB561, PIGT, CMPK1, LAP3, SQRDL, RPS27L, FAM82C, CNOT7, LL22NC03-5H6.5, SAV1, PSPC1, U2AF2, TMEM33, LEPREL1, TAPBPL, TMEM16A, MOSPD1, CHST12, METRN, C5orf23, PBK, MRPL46, FKBP14, C1GALT1, C7orf10, TRIM36, ARL6IP4, OGFOD2, GREM2, DENND2D, ELP3, C6orf15, GLS, USP3, C12orf52, ETV1, GPR177, AA058828*, DND1, AK023058*, SPATA5L1, RP3-377H14.5, MAP4, ISG20, RTN2, PRELP, DENND2A, FLJ10357, and CALML4;
• determining increases or decreases in the expression levels of the at least five genes in the second sample compared to the first sample;
• and
• identifying an agent that improves the prognosis of a subject having colon cancer based on said determining.

A method for determining a subject's predisposition to having colon cancer, said method comprising:

• obtaining a biological sample from the subject;
• detecting the expression level of at least five genes selected from a collection of 176 genes informative of colon cancer predisposition consisting of ACSL4, RQCD1, AA058828*, AIP, AKR1A1, AP3D1, ARL2BP, ARL4A, ARL6IP4, OGFOD2, ASNA1, ATP5B, C12orf52, C19orf36, C1GALT1, C1orf144, C5orf23, C6orf15, C7orf10, C8orf70, CALML4, CASP1, CCNA2, CCT2, CDC42BPA, AK023058*, CDR2L, CFB, CHST12, CLN5, CMPK1, CNOT7, CNPY2, COBL, COMMD4, COX5A, CXCL11, CYB561, CYB5B, DAZAP2, DDX23, DENND2A, DENND2D, DHX15, AL359599*, DND1, DOCK9, EGFR, ELP3, ERP29, ETV1, FAM82C, FDFT1, FKBP14, FLJ10357, FRYL, GALNS, GCHFR, GHITM, GLS, GPR177, GRB10, GREM2, GRHPR, GRP, GSR, GSTA1, H2AFZ, HOXB7, IFT88, IL15RA, ISG20, ITGAE, KIAA0746, SERINC2, KIF13B, KLC1, LAMP3, LANCL1, LAP3, LEPREL1, LL22NC03-5H6.5, LOC100131861, SAMM50, LRRC41, LRRC47, MAP4, MAPKAPK5, MCM5, MCRS1, METRN, METTL3, MFHAS1, MMP3, MOSPD1, MRPL46, MTUS1, MYRIP, N4BP2L2, NAB1, NAT1, NDUFC1, NISCH, NUMB, OGT, OSBPL3, PAM, PBK, PDGFA, PEBP1, PGDS, PIGR, PIGT, PRDM2, PULP, PSMA5, PSMD9, PSPC1, PTHLH, R3HCC1, RP3-377H14.5, RPLP0, RPLP0-like, RPS27L, RTN2, RYK, SAV1, SCAMP1, SERPINA1, SF3B1, SFPQ, SGCD, SLC25A3, SLC39A8, SMG7, SMURF2, SORD, SOX4, SPATA5L1, SQRDL, SRP72, SSNA1, STK3, SYNGR1, TAPBPL, TEGT, TES, TLN1, TMCC1, TMEM106C, TMEM16A, TMEM33, TMEM87A, TNFRSF10B, TNFSF10, TNIK, TRIM36, U2AF2, UBE2L6, UCP2, UNC84A, UQCRFS1, UQCRH, USP12, USP3, VPS41, WARS, WDR1, WDR68, XPO7, YBX1, ZC3H7B, ZMYM2, ZMYM5, ZNF117, and ZNF430;
• comparing the detected expression level of the at least five genes from said sample with the expression levels of the corresponding at least five genes when associated with a having a predisposition to colon cancer;
• and
• determining the subject's predisposition to having colon cancer based on said comparing.