Patent ID: 11959141
Assignee: FOUNDATION MEDICINE, INC.
Field: Computer technology (Electrical engineering)
Classification: CPC C  G | IPC C  G

Claim 3:
4. The method of claim 1, wherein the subgenomic interval from the malignant cell is chosen from a gene selected from the group consisting of ABCB1, ABCC2, ABCC4, ABCG2, ABI1, ABL1, ABL2, ACSL3, ACSL6, ACTB, ACVR1B, AF15Q14, AF1Q, AF3p21, AF5q31, AFF1, AFF4, AKAP9, AKT1, AKT2, AKT3, ALK, ALPHA, ALO17, ALOX12B, AMER1, APC, APCDD1, APH1A, AR, ARAF, ARFRP1, ARHGAP26, ARHGEF12, ARHH, ARID1A, ARID1B, ARID2, ARNT, ASPSCR1, ASMTL, ASXL1, ATF1, ATG5, ATIC, ATM, ATR, ATRX, ATXN1, AURKA, AURKB, AXIN1, AXL, B2M, BACH1, BAP1, BARD1, BCL10, BCL11A, BCL11B, BCL2, BCL2A1, BCL2L1, BCL2L2, BCL3, BCL5, BCL6, BCL7A, BCL9, BCOR, BCORL1, BCR, BIRC3, BLM, BRAF, BRCA1, BRCA2, BRD3, BRD4, BRIP1, BRSK1, BTG1, BTG2, BTK, BTLA, c1orf144, c11orf30, c12orf9, c15orf21, c17orf39, CAD, CALR, CAMTA1, CANT1, CARD11, CARS, CASP8, CBFA2T1, CBFA2T3, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CCT6B, CD22, CD247, CD36, CD58, CD70, CD74, CD79A, CD79B, CDC73, CDH1, CDH11, CDH2, CDH20, CDH5, CDK12, CDK4, CDK6, CDK8, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CDX2, CEBPA, CEP1, CHCHD7, CHD2, CHEK1, CHEK2, CHIC2, CHN1, CHTOP, CHUK, CIC, CIITA, CKS1B, CLP1, CLTC, CLTCL1, CMKOR1, CNTRL, COL1A1, COX6C, CPS1, CRBN, CREB1, CREB3L1, CREB3L2, CREBBP, CRKL, CRLF2, CRTC3, CSF1, CSF1R, CSF3R, CTCF, CTNNA1, CTNNB1, CUL4A, CUL4B, CUX1, CXCR4, CYP1B1, CYP17A1, CYP2C19, CYP2C8, CYP2D6, CYP3A4, CYP3A5, D10S170, DAXX, DDIT3, DDR1, DDR2, DDX5, DDX10, DDX3X, DDX6, DEK, DIS3, DKC1, DLEU2, DNM2, DNMT3A, DOT1L, DPYD, DTX1, DUSP2, DUSP22, DUSP9, DUX4, EBF1, ECT2L, EED, EGFR, EIF4A2, ELF4, ELK4, ELKS, ELL, ELN, ELP2, EML4, EMSY, EP300, EPHA3, EPHA5, EPHA6, EPHA7, EPHB1, EPHB4, EPHB6, EPOR, EPS15, ERBB2, ERBB3, ERBB4, ERCC2, ERG, ESR1, ESR2, ETS1, ETV1, ETV4, ETV5, ETV6, EVI1, EWSR1, EXOSC6, EZH2, FACL6, FAF1, FAM46C, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCL, FANG, FANCL, FANCM, FAS, FATS, FBXO11, FBXO31, FBXW7, FCGR2B, FCGR3A, FCRL4, FEV, FGF1, FGF10, FGF12, FGF14, FGF19, FGF23, FGF3, FGF4, FGF6, FGF7, FGFR1, FGFR1OP, FGFR2, FGFR3, FGFR4, FHIT, FIP1L1, FLCN, FLI1, FLT1, FLT3, FLT4, FLU, FLYWCH1, FNBP1, FOP, FOXL2, FOXO1, FOXO3, FOXO3A, FOXO4, FOXO1A, FOXP1, FOXP4, FRS2, FSTL3, FUS, FVT1, GADD45B, GAS7, GATA1, GATA2, GATA3, GID4, GLI1, GLIS2, GMPS, GNA11, GNA12, GNA13, GNAQ, GNAS, GOLGA5, GOPC, GPHN, GPR124, GRAF, GRIN2A, GSK3B, GSTP1, GTSE1, GUCY1A2, H4, HCMOGT-1, HDAC1, HDAC4, HDAC7, HEAB, HEM, HERPUD1, HEY1, HGF, HIP1, HIST1H1A, HIST1H1C, HIST1H1D, HIST1H1E, HIST1H2AC, HIST1H2AG, HIST1H2AL, HIST1H2AM, HIST1H2BC, HIST1H2BJ, HIST1H2BK, HIST1H2BO, HIST1H3B, HIST1H4I, HLA-A, HLF, HLXB9, HMGA1, HMGA2, HNF1A, HNRNPA2B1, HOOKS, HOX11, HOXA11, HOXA13, HOXA3, HOXA9, HOXC11, HOXC13, HOXD11, HOXD13, HRAS, HSP90AA1, HSP90AB1, HSPCA, HSPCB, ICK, ID3, IDH1, IDH2, IGF1, IGF1R, IGF2, IGF2R, IGH, IGK, IGL, IKBKE, IKZF1, IKZF2, IKZF3, IL2, IL21R, IL3, IL7R, INHBA, INPP4B, INPP5D, INSR, IRF1, IRF4, IRF8, IRS2, IRTA1, ITPA, ITK, JAK1, JAK2, JAK3, JARID2, JAZF1, JUN, KAT6A, KDM2B, KDM4C, KDM5A, KDM5C, KDM6A, KDR, KDSR, KEAP1, KIF5B, KIT, KLHL6, KIAA1549, KLK2, KMT2A, KMT2B, KMT2C, KRAS, KTN1, LAF4, LASP1, LCK, LCP1, LCX, LEF1, LHFP, LHX4, LIFR, LMO1, LMO2, LPP, LRP1B, LRP2, LRP6, LRRK2, LTK, LYL1, MAF, MAFB, MAGEA5, MAGED1, MALT1, MAML2, MAN1B1, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAP3K13, MAP3K14, MAP3K6, MAP3K7, MECT1, MCL1, MDM2, MDM4, MDS1, MDS2, MECOM, MECT1, MED12, MEF2B, MEF2C, MEN1, MET, MHC2TA, MIB1, MITF, MKI67, MKL1, MKL2, MLF1, MLH1, MLL2, MLLT1, MLLT10, MLLT2, MLLT3, MLLT4, MLLT6, MLLT7, MLST8, MN1, MNX1, MORF, MPL, MRE11A, MSF, MSH2, MSH3, MSH6, MSI2, MSN, MTAP, MTCP1, MTHFR, MTOR, MUC1, MUTYH, MYB, MYC, MYCL, MYCL1, MYCN, MYD88, MYH11, MYH9, MYO18A, MYST3, MYST4, NACA, NBEAP1, NBN, NCOA1, NCOA2, NCOA4, NCOR1, NCOR2, NCSTN, NDRG1, NF1, NF2, NFE2L2, NFIB, NFKBIA, NFKB1, NFKB2, NFKBIE, NIN, NKX2-1, NOD1, NONO, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NPM1, NQO1, NR4A3, NRP2, NRAS, NSD1, NT5C2, NTRK1, NTRK2, NTRK3, NUMA1, NUP214, NUP93, NUP98, NUT, NUTM2A, OLIG2, OMD, P2RY8, PAFAH1B2, PAG1, PAK3, PAK7, PALB2, PARP1, PARP2, PARP3, PARP4, PALB2, PASK, PAX3, PAX5, PAX7, PAX8, PBRM1, PBX1, PC, PCBP1, PCLO, PCM1, PCSK7, PDCD1, PDCD11, PDCD1LG2, PDE4DIP, PDGFB, PDGFRA, PDGFRB, PDK1, PDL1, PER1, PHF1, PHF6, PHLPP2, PHOX2B, PICALM, PIK3C2G, PIK3C3, PIK3CA, PIK3CG, PIK3R1, PIK3R2, PIM1, PKHD1, PLAG1, PLCG1, PLCG2, PML, PMS2, PMX1, PNRC1, PNUTL1, POT1, POU2AF1, POU5F1, PPARG, PPP1CB, PPP2R1A, PRCC, PRDM1, PRDM16, PRKAR1A, PRKDC, PRRX1, PRO1073, PRSS8, PSIP1, PSIP2, PTCH1, PTCH2, PTEN, PTK2, PTK2B, PTK7, PTPN11, PTPN2, PTPN6, PTPRD, PTPRO, RAB5EP, RABEP1, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD51L1, RAD52, RAD54L, RAF1, RALGDS, RANBP17, RAP1GDS1, RARA, RASGEF1A, RB1, RBM15, RCOR1, REL, RELN, RET, RHEB, RHOA, RHOH, RICTOR, RMRP, RNF213, RNF43, ROCK1, ROS1, RPA1, RPL11, RPL13, RPL15, RPL22, RPL35A, RPN1, RPS14, RPS15, RPS19, RPS26, RPTOR, RUNX1, RUNX1T1, RUNX2, RUNXBP2, RUNXT1, S1PR2, SBDS, SDHA, SDHB, SDHC, SDHD, SEC31A, SEPT5, SEPT6, SEPT9, SERP2, SET, SETBP1, SETD2, SF3B1, SFPQ, SFRS3, SGK1, SH2B3, SH3GL1, SIL, SLC1A2, SLC19A1, SLC22A2, SLC45A3, SLCO1B3, SMAD2, SMAD3, SMAD4, SMARCA1, SMARCA4, SMARCB1, SMARCD1, SMC1A, SMC3, SMO, SNX29, SPOP, SOCS1, SOCS2, SOCS3, SOD2, SOX10, SOX2, SPEN, SPOP, SRC, SRGAP3, SRSF2, SRSF3, SS18, SS18L1, SSH3BP1, SSX1, SSX2, SSX4, STAG2, STAT5, STAT4, STAT5A, STAT5B, STAT6, STK11, STK12, STL, SUFU, SULT1A1, SUZ12, SYK, TAF1, TAF15, TAL1, TAL2, TBL1XR1, TBX22, TBX23, TBX3, TCEA1, TCF12, TCF3, TCL1A, TCL6, TEC, TET1, TET2, TFE3, TFEB, TFG, TFPT, TFRC, TGFBR2, THRAP3, TIF1, TIPARP, TLL2, TLX1, TLX3, TMEM30A, TMPRSS2, TMSB4XP8, TNFAIP3, TNFRSF11A, TNFRSF14, TNFRSF17, TNFSF9, TNKS, TNKS2, TOP1, TP53, TP63, TPM3, TPM4, TPMT, TPR, TRA, TRAF2, TRAF3, TRAF5, TRB, TRD, TRG, TRIM24, TRIM27, TRIM33, TRIP11, TRRAP, TSC, TSC1, TSC2, TSHR, TTL, TUSC3, TYK2, TYMS, U2AF1, U2AF2, UG T1A1, UMPS, USP6, USP9X, VHL, WDR90, WHSC1, WHSC1L1, WISPS, WT1, XBP1, XPO1, XRCC3, YPEL5, YY1AP1, ZBTB16, ZMYM2, ZMYM3, ZNF145, ZNF198, ZNF217, ZNF24, ZNF278, ZNF331, ZNF384, ZNF521, ZNF703, ZNF9, ZNFN1A1, ZRSR2, and an MHC gene.