Table A1.
(a) Comprehensive Cancer Next Generation Sequencing (NGS) Panel DNA gene list (543 genes). Only CNV analysis or ^—Internal Tandem Duplication (ITD) interrogated; $—Exon 1 region not entirely sequenced [11,12]. (b) Comprehensive Cancer Next Generation Sequencing (NGS) Panel RNA gene list (183 genes) * CTNNB1 exon—level (large) deletions, ^—EGFRvIII, and $—MET exon 14 skipping variant interrogated in addition to gene fusion [12].
| (a) | |||||||||
| ABL1 | ABL2 | ABRAXAS1 * | ACVR1 | ACVR1B * | ADGRA2 * | AIP | AKT1 | AKT2 | AKT3 |
| ALK | AMER1 | APC | AR | ARAF | ARFRP1 * | ARID1A | ARID1B $ | ARID2 | ASXL1 |
| ATM | ATR | ATRX | AURKA | AURKB | AXIN1 | AXIN2 | AXL | B2M | BAP1 |
| BARD1 | BCL10 * | BCL11B * | BCL2 | BCL2L1 * | BCL2L2 * | BCL6 | BCL7A | BCOR ^ | BCORL1 |
| BIRC3 | BLM | BMPR1A | BRAF | BRCA1 | BRCA2 | BRCC3 * | BRD3 * | BRD4 | BRINP3 * |
| BRIP1 | BTG1 | BTK | BUB1B * | C19MC | CALR | CARD11 | CASP8 * | CBFB | CBL |
| CBLB | CBLC | CCN6 | CCND1 | CCND2 | CCND3 | CCNE1 | CD19 * | CD274 | CD28 * |
| CD40 * | CD58 | CD79A | CD79B | CDC73 | CDH1 | CDK12 | CDK4 | CDK6 | CDK8 |
| CDKN1A | CDKN1B | CDKN1C | CDKN2A | CDKN2B | CDKN2C | CEBPA | CHD2 | CHD4 | CHEK1 |
| CHEK2 | CIC | CIITA * | COL1A1 | CREBBP | CRKL | CRLF2 | CSF1R | CSF3R | CSNK1A1 * |
| CTCF | CTLA4 * | CTNNA1 * | CTNNB1 | CUL3 | CUX1 | CXCR4 | CYLD | DAXX | DDR2 |
| DDX3X | DDX41 | DGCR8 | DICER1 | DIS3L2 | DKC1 | DNM2 | DNMT3A | DOT1L | DROSHA |
| EBF1 | EED | EFNB2 * | EGFR | EGR2 * | EIF1AX | ELOC | EMSY * | EP300 | EPCAM |
| EPHA3 | EPHA5 | EPHA7 * | EPHB1 | EPHB4 * | ERBB2 | ERBB3 | ERBB4 | ERCC1 * | ERCC2 |
| ERCC3 * | ERCC4 * | ERCC5 * | ERG * | ERRFI1 * | ESR1 | ETNK1 | ETS1 * | ETV1 * | ETV4 * |
| ETV5 * | ETV6 | EWSR1 * | EXT1 | EXT2 | EZH2 | FANCA | FANCB | FANCC | FANCD2 * |
| FANCE * | FANCF * | FANCG * | FANCI | FANCL * | FANCM * | FAS | FAT1 | FAT3 * | FBXO11 |
| FBXW7 | FGF10 * | FGF14 * | FGF19 | FGF23 * | FGF3 | FGF4 | FGF6 * | FGFR1 | FGFR2 |
| FGFR3 | FGFR4 | FH | FLCN | FLT1 | FLT3 ^ | FLT4 | FOXA1 | FOXL2 | FOXO1 * |
| FOXP1 | FOXR2 * | FRK | FRS2 * | FUBP1 | FUS * | GABRA6 * | GATA1 | GATA2 | GATA3 |
| GATA4 * | GATA6 * | GEN1 * | GID4 * | GLI1 | GLI2 | GNA11 | GNA13 | GNA14 | GNAQ |
| GNAS | GNB1 | GPC3 * | GREM1 * | GRIN2A | GRM3 * | GSK3B | H1-4 | H3-3A | H3-3B |
| H3C2 | H3C3 | HDAC4 | HDAC9 | HGF | HIF1A | HMGA2 * | HNF1A | HOXB13 * | HRAS |
| HSD3B1 | HSP90AA1 * | ID3 | IDH1 | IDH2 | IGF1R | IGF2 * | IKBKE | IKZF1 | IKZF2 |
| IKZF3 | IL2RG * | IL6ST | IL7R | INHBA * | INPP4B | IRF2 | IRF4 | IRF8 * | IRS2 * |
| ITK * | ITPKB * | JAK1 | JAK2 | JAK3 | JAZF1 * | JUN * | KAT6A * | KBTBD4 | KCNJ5 |
| KDM4C | KDM5A | KDM5C | KDM6A | KDR | KEAP1 | KEL * | KIF1B * | KIF5B * | KIT |
| KLF2 | KLF4 | KLHL6 * | KMT2A | KMT2B | KMT2C | KMT2D | KRAS | LEF1 | LIFR * |
| LMO1 | LRP1B * | LYN * | LYST * | LZTR1 | MAGI2 * | MAML2 * | MAP2K1 | MAP2K2 | MAP2K4 |
| MAP3K1 | MAP3K14 | MAP3K3 * | MAP3K7 * | MAPK1 | MAPK3 | MAX | MCL1 | MDM2 | MDM4 |
| MECOM | MED12 | MEF2B | MEN1 | MET | MITF | MLH1 | MLH3 | MLLT1 | MN1 |
| MPL | MRE11 | MSH2 | MSH3 | MSH6 | MTOR | MUTYH | MYB | MYBL1 | MYC |
| MYCL * | MYCN | MYD88 | MYH9 * | MYOD1 | NBN | NCOA2 * | NCOR1 | NCOR2 | NF1 |
| NF2 | NFE2 | NFE2L2 | NFKBIA | NFKBIE | NKX2-1 | NOTCH1 | NOTCH2 | NOTCH3 | NPM1 |
| NRAS | NSD1 | NSD2 | NT5C2 | NTHL1 | NTRK1 | NTRK2 | NTRK3 | NUP214 * | NUP93 * |
| NUTM1 * | OTX2 | PAK3 | PALB2 | PAX3 * | PAX5 | PAX7 * | PAX8 * | PBRM1 | PDCD1 |
| PDCD1LG2 * | PDGFB * | PDGFRA | PDGFRB | PDK1 * | PHF6 | PHOX2B | PIGA | PIK3C2B * | PIK3CA |
| PIK3CB | PIK3CD | PIK3CG | PIK3R1 | PIK3R2 | PIM1 | PLAG1 * | PLCG1 | PLCG2 | PML * |
| PMS1 | PMS2 | POLD1 * | POLE | POLR2A | POT1 | PPARG * | PPM1D | PPP2R1A | PRDM1 |
| PREX2 | PRKAR1A | PRKCA | PRKCI * | PRKDC | PRKN | PRPF40B | PRPF8 | PRSS8 * | PTCH1 |
| PTEN | PTPN11 | PTPRD | PTPRT | QKI * | RAB35 * | RAC1 | RAD21 | RAD50 | RAD51 |
| RAD51B | RAD51C | RAD51D | RAF1 | RANBP2 * | RARA * | RASA1 | RB1 | RBM10 | RECQL * |
| RECQL4 * | REL * | RELA * | RET | RHOA | RICTOR | RINT1 * | RIT1 | RNF43 | ROS1 * |
| RPS15 | RPS19 | RPS20 * | RPS6KA3 | RPTOR | RRAGC | RSPO2 * | RSPO3 * | RUNX1 | RUNX1T1 * |
| SAMD9 | SAMD9L | SBDS * | SDHA | SDHAF2 | SDHB | SDHC | SDHD | SETBP1 | SETD2 |
| SF1 | SF3A1 | SF3B1 | SGK1 | SH2B3 | SIX1 | SIX2 | SLIT2 * | SLX4 | SMAD2 |
| SMAD3 | SMAD4 | SMARCA4 | SMARCB1 | SMARCE1 | SMC1A | SMC3 | SMO | SNCAIP * | SOCS1 |
| SOS1 | SOX10 * | SOX2 | SOX9 * | SPEN | SPOP | SPTA1 | SRC | SRP72 | SRSF2 |
| SS18 * | STAG2 | STAT3 | STAT4 * | STAT5B | STAT6 | STK11 | SUFU | SUZ12 | SYK * |
| TAF1 | TBL1XR1 | TBX3 | TBXT * | TCF12 | TCF3 | TCF7L2 | TEK | TENT5C * | TERC |
| TERT | TET1 * | TET2 | TFE3 * | TFEB * | TGFBR2 | TMEM127 | TMPRSS2 * | TNFAIP3 | TNFRSF14 |
| TOP1 | TOP2A * | TP53 | TP63 | TPMT * | TRAF3 | TRAF7 | TRRAP | TSC1 | TSC2 |
| TSHR | TYK2 | U2AF1 | U2AF2 | USP6 * | USP7 | VAV1 | VEGFA | VHL | WRN |
| WT1 | XPC * | XPO1 | XRCC2 * | YAP1 * | YWHAE * | ZBTB2 * | ZFTA * | ZMYM3 | ZNF217 * |
| ZNF703 * | ZNF750 | ZRSR2 | |||||||
| (b) | |||||||||
| ABL1 | ABL2 | AKT3 | ALK | ARHGAP26 | AXL | BCL10 | BCL11B | BCL2 | BCL6 |
| BCOR | BCORL1 | BCR | BIRC3 | BRAF | BRD3 | BRD4 | BTG1 | C11ORF95 | CAMTA1 |
| CARD11 | CBFB | CBL | CCND1 | CCND3 | CDK6 | CHIC2 | CIC | CIITA | COL1A1 |
| CREBBP | CRLF2 | CSF1R | CTNNB1 * | DEK | DNAJB1 | DUSP22 | EBF1 | EGFR ^ | EP300 |
| EPC1 | EPOR | ERBB2 | ERG | ETV1 | ETV4 | ETV5 | ETV6 | EWSR1 | FER |
| FGFR1 | FGFR2 | FGFR3 | FGR | FLT3 | FOS | FOSB | FOXO1 | FOXP1 | FOXR2 |
| FUS | GLI1 | GLI2 | GLIS2 | HLF | HMGA2 | HTRA1 | IKZF1 | IKZF2 | IKZF3 |
| IRF4 | ITK | JAK1 | JAK2 | JAK3 | JAZF1 | KAT6A | KIF5B | KLF2 | KMT2A |
| LMO1 | LYN | MALT1 | MAML2 | MAST1 | MAST2 | MEAF6 | MECOM | MEF2D | MET $ |
| MKL1 | MKL2 | MLLT10 | MLLT4 | MN1 | MSMB | MYB | MYBL1 | MYC | MYH11 |
| MYH9 | NCOA1 | NCOA2 | NCOA3 | NF1 | NF2 | NFKB2 | NOTCH1 | NOTCH2 | NPM1 |
| NR4A3 | NRG1 | NSD1 | NTRK1 | NTRK2 | NTRK3 | NUMBL | NUP214 | NUP98 | NUTM1 |
| PAG1 | PAX3 | PAX5 | PAX7 | PAX8 | PDCD1LG2 | PDGFB | PDGFRA | PDGFRB | PHF1 |
| PIK3CA | PKN1 | PLAG1 | PML | PPARG | PRDM1 | PRDM16 | PRKACA | PRKCA | PRKCB |
| PTCH1 | PTK2B | PVT1 | QKI | RAF1 | RARA | RELA | RET | ROS1 | RSPO2 |
| RSPO3 | RUNX1 | RUNX1T1 | SETD2 | SS18 | SSX1 | SSX2 | SSX4 | STAT6 | SUZ12 |
| SYK | TAF15 | TAL1 | TBL1XR1 | TCF12 | TCF3 | TERT | TET1 | TFE3 | TFEB |
| TFG | THADA | TMPRSS2 | TOP1 | TP63 | TYK2 | USP6 | VGLL2 | WHSC1 | YAP1 |
| YWHAE | ZCCHC7 | ZNF384 | |||||||