GENE EXPRESSION MARKERS OF ONCOLYTIC VIRUS SENSITIVITY
First Claim
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1. A method, comprising:
- determining an expression level for each of a plurality of genes in a tumor sample obtained from a patient;
calculating a total predictor score based on the expression levels for each of the plurality of genes; and
predicting, if the total predictor score satisfies a first predictor score threshold, that an oncolytic virus treatment for the tumor would have efficacy, and if the total predictor score satisfies a second predictor score threshold, that the oncolytic virus treatment for the tumor would lack efficacy.
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Abstract
A method of predicting an efficacy of an oncolytic virus treatment for a tumor comprises calculating a single-gene predictor score for each of a plurality of genes; calculating a predictor score from the sum of the single-gene predictor scores for the plurality of genes; and predicting, if the predictor score is greater than a predictor score threshold, that the treatment would have efficacy, and if the predictor score is less than a predictor score threshold, that the treatment would lack efficacy. Also, methods of predicting an efficacy of a treatment for a tumor comprise identifying the type and subtype of the tumor, wherein the efficacy of the treatment for the type and subtype of the tumor is known.
3 Citations
16 Claims
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1. A method, comprising:
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determining an expression level for each of a plurality of genes in a tumor sample obtained from a patient; calculating a total predictor score based on the expression levels for each of the plurality of genes; and predicting, if the total predictor score satisfies a first predictor score threshold, that an oncolytic virus treatment for the tumor would have efficacy, and if the total predictor score satisfies a second predictor score threshold, that the oncolytic virus treatment for the tumor would lack efficacy. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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10. A kit for predicting an efficacy of an oncolytic virus treatment for a tumor, the kit comprising:
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reagents for measuring an expression level for each of a plurality of genes in a tumor sample obtained from a patient, wherein the plurality of genes comprises at least two of; ABI3BP, AGXT2L2, AKR1C1, ANKRD5, ANLN, ANO10, ANTXR2, ANXA1, ARC, ARL2, ATF7IP, ATP6V0A2, ATRIP, AUTS2, AXGT2L2, BAD, BCL9L, BLM, BR13, C10orf11, C14orf106, C14orf45, C15orf5, C17orf76, C1orf115, C1orf31, C20orf134, C20orf88, C21orf91, C2orf88, C4orf32, C6orf226, C7orf31, C7org106, CA14, CALCOCO2, CBX5, CBX6, CCDC109B, CCDC30, CCDC45, CD44, CD83, CDK5R1, CEP152, CHD1, CHKA, CPT1C, CPVL, CTSA, CYP4V2, DAPK1, DCDC2, DDX60L, DEPDC7, DHX33, DNM1L, DUS1L, EHD2, ETV2, F2R, F8, FAM129B, FAM174B, FAM178A, FIBP, FKBP10, FLJ10213, FSCN1, FSTL5, FTO, GALNT3, GARNL4, GMPR, GNA12, GPR137B, GPR143, GPX4, GPX7, hCG 20036, HHAT, HIST1H2BH, HK1, HMGA2, HOOK1, HOXA10, HOXA13, HOXA3, HOXA5, HOXA6, HOXB7, HOXB9, HOXB9K, HPS4, ICAM3, IGFBP3, IKAA1324L, IL12RB2, INTS2, ITGA5, ITGA7, ITM2C, ITPKB, IVNS1ABP, KCNA4, KCNK1, KCNN4, KCTD17, KIAA0355, KIAA0652, KIAA1324, KIAA1598, KIF23, LINS1, LOC152217, LOC202781, LOC401068, LPPR2, LRRC29, LVN, MAGEH1, MAN1B1, MAP4K3, MAPKAPK3, MBL1P1, MECOM, MED16, MEPCE, MESDC1, MFAP2, MGAT4A, MICAL3, MOSC2, MOSPD1, MRS2, MVP, MYADM, MYOM2, NCALD, NCOA6, NDRG1, NDUFV1, NEIL2, NELL1, NEO1, NFASC, NFIC, NINL, NME5, NNMT, NOL3, NR1D1, NRP1, NUDT22, OSCP1, OTUB1, PAEP, PCDH18, PCDH96, PCDHB11, PCDHB16, PCDHB2, PCDHB6, PCDHB8, PCF11, PDCD2, PDCHB11, PDE8A, PFTK1, PGBD5, PGLYRP2, PHLPP2, PHPT1, PHYH, PITPNM1, PLAG1, PLCL2, PNLPA6, POGK, POLD4, POLDIP2, PPAP2C, PPM1H, PPP2R1A, PRRX1, PTMS, PTRF, PUM2, PUS3, RAB11FIP4, RAB15, RAB17, RAB1B, RABG1G, RASSF8, RBMS3, RC3H1, RCOR3, RGS10, RGS20, RNF187, ROM1, RRAS, RSPO3, RTN4, SB3BGRL3, SEMA6A, SEPT3, SERGEF, SERPINH1, SFRS15, SH3BGRL3, SH3YL1, SKA2, SLC16A6, SLC17A5, SLC27A3, SLC2A3P1, SLC44A3, SMOX, SNAPC2, SNX21, SORBS1, SOX8, SP4, SPAG4, SPAG9, ST6GALNAC, SUMF2, SYCP2, TBRG1, THBS3, THYN1, TIK2, TK1, TK2, TM4SF18, TMEM170B, TMEM60, TNFRSF1A, TNKS1BP1, TOB1, TOM1, TRPC3, TRPS1, TSC22D3, TTYH2, TUG1, UBASH3B, UBXN6, WNT5A, WT1, ZBTB41, ZBTB47, ZEB1, ZFP36L1, ZMYM2, ZNF138, ZNF175, ZNF195, ZNF280C, ZNF462, ZNF561, or ZXDB. - View Dependent Claims (11, 12, 13)
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14. A method, comprising:
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determining an expression level for each of a plurality of genes in a tumor sample by at least one of northern blotting, in situ hybridization, RNAse protection assay, reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR, use of an antibody to DNA duplexes, use of an antibody to RNA duplexes, use of an antibody to DNA-RNA hybrid duplexes, use of an antibody to DNA-protein duplexes, Serial Analysis of Gene Expression (SAGE), gene expression analysis by massively parallel signature sequencing (MPSS), a microarray, southern blotting, western blotting, ELISA-like assays, quantum-dot gene expression analysis, or direct digital detection for gene expression analysis, wherein the plurality of genes comprises at least two of; ABI3BP, AGXT2L2, AKR1C1, ANKRD5, ANLN, ANO10, ANTXR2, ANXA1, ARC, ARL2, ATF7IP, ATP6V0A2, ATRIP, AUTS2, AXGT2L2, BAD, BCL9L, BLM, BR13, C10orf11, C14orf106, C14orf45, C15orf5, C17orf76, C1orf115, C1orf31, C20orf134, C20orf88, C21orf91, C2orf88, C4orf32, C6orf226, C7orf31, C7org106, CA14, CALCOCO2, CBX5, CBX6, CCDC109B, CCDC30, CCDC45, CD44, CD83, CDK5R1, CEP152, CHD1, CHKA, CPT1C, CPVL, CTSA, CYP4V2, DAPK1, DCDC2, DDX60L, DEPDC7, DHX33, DNM1L, DUS1L, EHD2, ETV2, F2R, F8, FAM129B, FAM174B, FAM178A, FIBP, FKBP10, FLJ10213, FSCN1, FSTL5, FTO, GALNT3, GARNL4, GMPR, GNA12, GPR137B, GPR143, GPX4, GPX7, hCG 20036, HHAT, HIST1H2BH, HK1, HMGA2, HOOK1, HOXA10, HOXA13, HOXA3, HOXA5, HOXA6, HOXB7, HOXB9, HOXB9K, HPS4, ICAM3, IGFBP3, IKAA1324L, IL12RB2, INTS2, ITGA5, ITGA7, ITM2C, ITPKB, IVNS1ABP, KCNA4, KCNK1, KCNN4, KCTD17, KIAA0355, KIAA0652, KIAA1324, KIAA1598, KIF23, LINS1, LOC152217, LOC202781, LOC401068, LPPR2, LRRC29, LVN, MAGEH1, MAN1B1, MAP4K3, MAPKAPK3, MBL1P1, MECOM, MED16, MEPCE, MESDC1, MFAP2, MGAT4A, MICAL3, MOSC2, MOSPD1, MRS2, MVP, MYADM, MYOM2, NCALD, NCOA6, NDRG1, NDUFV1, NEIL2, NELL1, NEO1, NFASC, NFIC, NINL, NME5, NNMT, NOL3, NR1D1, NRP1, NUDT22, OSCP1, OTUB1, PAEP, PCDH18, PCDH96, PCDHB11, PCDHB16, PCDHB2, PCDHB6, PCDHB8, PCF11, PDCD2, PDCHB11, PDE8A, PFTK1, PGBD5, PGLYRP2, PHLPP2, PHPT1, PHYH, PITPNM1, PLAG1, PLCL2, PNLPA6, POGK, POLD4, POLDIP2, PPAP2C, PPM1H, PPP2R1A, PRRX1, PTMS, PTRF, PUM2, PUS3, RAB11FIP4, RAB15, RAB17, RAB1B, RABG1G, RASSF8, RBMS3, RC3H1, RCOR3, RGS10, RGS20, RNF187, ROM1, RRAS, RSPO3, RTN4, SB3BGRL3, SEMA6A, SEPT3, SERGEF, SERPINH1, SFRS15, SH3BGRL3, SH3YL1, SKA2, SLC16A6, SLC17A5, SLC27A3, SLC2A3P1, SLC44A3, SMOX, SNAPC2, SNX21, SORBS1, SOX8, SP4, SPAG4, SPAG9, ST6GALNAC, SUMF2, SYCP2, TBRG1, THBS3, THYN1, TIK2, TK1, TK2, TM4SF18, TMEM170B, TMEM60, TNFRSF1A, TNKS1BP1, TOB1, TOM1, TRPC3, TRPS1, TSC22D3, TTYH2, TUG1, UBASH3B, UBXN6, WNT5A, WT1, ZBTB41, ZBTB47, ZEB1, ZFP36L1, ZMYM2, ZNF138, ZNF175, ZNF195, ZNF280C, ZNF462, ZNF561, or ZXDB. - View Dependent Claims (15, 16)
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Specification