Table 3.
Melanoma cohorts with clinical NGS testing.
| # of samples | Population | Yield | Panel size (genes) | Reference |
|---|---|---|---|---|
| 699 | Cutaneous melanoma (including acral), mucosal melanoma, uveal melanoma; United States (somatic) | 556/699 (80%) | 46 ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNAS, HNF1A, HRAS, IDH1, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL |
(91) |
| 132 patients | Cutaneous (including acral lentiginous melanoma, melanoma in blue nevus), uveal melanoma, mucosal melanoma; United Kingdom (somatic) | 93/132 (70%) | 7 BRAF, GNA11, GNAQ, KIT, KRAS, MAP2K1, NRAS |
(92) |
| 121 | Cutaneous melanoma; United States (somatic) | 104/121 (86%) | 50 ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL |
(93) |
| 100 | Cutaneous melanomas; Spain (somatic) | 85/100 (85%) | 35 ADAMST18, ALK, BPA1, BRAF, CDK4, CDKN2A, EPHA7, ERBB4, GNA11, GNAQ, GRIN2A, GRM3, HOXD8, HRAS, IRS4, KIT, KRAS, MAP2K1, MAP2K2, MC1R, MET, MITF, NF1, NRAS, PIK3CA, PPP6C, PREX2, PTEN, RAC1, STK11, STK19, STK31, TAF1L, TERT, TRRRAP |
(94) |
| 71 | Mucosal melanomas; Germany (somatic) | 50/71 (70%) | 29 ARID1A, ARID2, BAP1, BRAF, CDK4, CDKN2A, CTNNB1, EZH2, FBXW7, GNA11, GNAQ, HRAS, IDH1, KIT, KRAS, MAP2K1, MAP2K2, MITF, NF1, NRAS, PIK3CA, PIK3R1, PTEN, RAC1, SF3B1, SMARCA4, TERT, TP53, WT1 |
(95) |
| 36 | BRAF wild-type recurred or metastatic melanoma (acral); Korea (somatic) | 33/36 (92%) | 225 ABL1, ABL2, AKT1, AKT2, AKT3, ALK, APC, AR, ARAF, ARID1A, ATM, ATR, AURKA, AURKB, AURKC, AXL, BAP1, BARD1, BCL2, BRAF, BRCA1, BRCA2, BRIP1, BTK, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CDH1, CDK1, CDK4, CDK6, CDK11B, CDK12, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CEBPA, CHEK1, CHEK2, CREBBP, CSF1R, CTNNB1, DDR1, DDR2, DICER1, DNMT3A, DOT1L, DPYD, EGFR, EIF1AX, EMSY, EP300, EPCAM, EPHA3, ERBB2, ERBB3, ERBB4, ERCC2, ERG, ESR1, ETV1, EWSR1, EZH2, FAM175A, FANCA, FANCC, FANCD2, FANCG, FANCI, FANCL, FANCM, FBXW7, FGF3, FGF4, FGF6, FGF10, FGF14, FGF19, FGF23, FGFR1, FGFR2, FGFR3, FGFR4, FLT1, FLT3, FLT4, FOXA1, FOXL2, GNA11, GNAQ, GNAS, GNB2L1, HDAC1, HDAC9, HGF, HRAS, IDH1, IDH2, IGF1R, IGF2, IGFBP3, INPP4B, IRF1, JAK1, JAK2, JAK3, JUN, KDM5C, KDM6A, KDR, KEAP1, KIT, KMT2D, KRAS, LATS1, LATS2, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAP3K4, MAPK1, MAPK8, MCL1, MDM2, MDM4, MET, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYC, MYCN, NEK2, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NPM1, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PAK2, PALB2, PARP1, PARP2, PBRM1, PDGFB, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PIK3CD, PIK3R1, PIK3R2, PMS2, POLD1, POLE, POLQ, PPARG, PPP2R2A, PRKCB, PTEN, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RB1, RBM10, RELA, RET, RHEB, RICTOR, RIT1, RNF43, ROS1, RPTOR, RSPO1, SDHB, SDK1, SETD2, SMAD4, SMARCA4, SMARCB1, SMG1, SOX2, SPOP, SQSTM1, SRC, SS18, STAT1, STAT6, STK11, SUMO1, SYK, TERT, TFE3, TOP2A, TP53, TP63, TPMT, TSC1, TSC2, TSHR, UGT1A1, VHL, XRCC2, ZBTB16 |
(96) |
| 30 | Melanoma metastases; United States (somatic) | 30/30 (100%) | 182 ABL1, ABL2, AKT1, AKT2, AKT3, ALK, APC, AR, ARAF, ARFRP1, ARID1A, ATM, ATR, AURKA, AURKB, BAP1, BCL2, BCL2A1, BCL2L1, BCL2L2, BCL6, BRAF, BRCA1, BRCA2, CARD11, CBL, CCND1, CCND2, CCND3, CCNE1, CD79A, CD79B, CDH1, CDH2, CDH5, CDH20, CDK4, CDK6, CDK8, CDKN2A, CDKN2B, CDKN2C, CEBPA, CHEK1, CHEK2, CRKL, CRLF2, CTNNB1, DDR2, DNMT3A, DOT1L, EGFR, EPHA3, EPHA5, EPHA6, EPHA7, EPHB1, EPHB4, EPHB6, ERBB2, ERBB3, ERBB4, ERCC2, ERG, ESR1, EZH2, FANCA, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FLT1, FLT3, FLT4, FOXP4, GATA1, GNA11, GNAQ, GNAS, GPR124, GUCY1A2, HOXA3, HRAS, HSP90AA1, IDH1, IDH2, IGF1R, IGF2R, IKBKE, IKZF1, INHBA, INSR, IRS2, JAK1, JAK2, JAK3, JUN, KDM6A, KDR, KIT, KRAS, LRP1B, LRP6, LTK, MAP2K1, MAP2K2, MAP2K4, MCL1, MDM2, MDM4, MEN1, MET, MITF, MLH1, MLL, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYC, MYCL1, MYCN, NF1, NF2, NKX2-1, NOTCH1, NPM1, NRAS, NTRK1, NTRK2, NTRK3, PAK3, PAX5, PDGFRA, PDGFRB, PHLPP2, PIK3CA, PIK3CG, PIK3R1, PKHD1, PLCG1, PRKDC, PTCH1, PTCH2, PTEN, PTPN11, PTPRD, RAF1, RARA, RB1, RET, RICTOR, RPTOR, RUNX1, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMO, SOX2, SOX10, SRC, STAT3, STK11, SUFU, TBX22, TET2, TGFBR2, TNFAIP3, TNKS, TNKS2, TOP1, TP53, TSC1, TSC2, USP9X, VHL, WT1 |
(97) |
| 18 | Cutaneous melanoma (metastatic); United States (somatic) | 16/18 (89%) | 248 ABCB1, ABL1, ABL2, ADRB1, ADRB2, AKT1, AKT2, AKT3, ALK, ALOX5, APC, APC2, AR, ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID4A, ARID4B, ARID5A, ARID5B, ASXL1, ATM, ATR, AURKA, BCL2, BCR, BRAF, BRCA1, BRCA2, BRD4, CBL, CBLB, CCND1, CCNE1, CDC73, CDH1, CDH6, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CEBPA, CHD5, CHEK1, CHEK2, COBRA1, COMT, CREBBP, CRKL, CSF1R, CTNNB1, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DNMT3A, DPYD, DRD2, EGFR, EPHA3, EPHA5, EPHA6, EPHA10, EPHB6, ERBB2, ERBB3, ERBB4, ERCC1, ERG, FAM123B, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FHIT, FKBP9, FLT1, FLT3, FLT4, FOLR1, G6PD, GATA3, GNA11, GNAQ, GNAS, GSTM1, GSTP1, GSTT1, GUCY1A2, H3F3A, H3F3B, HECW1, HLA-A, HLA-B, HNF1A, HRAS, HSP90AA1, IDH1, IDH2, IGF1R, IKBKE, IKZF1, IL28B, ITPA, JAK1, JAK2, JAK3, JARID2, KCNH2, KCNJ11, KDM5A, KDM5B, KDM5C, KDM6A, KDR, KEAP1, KIT, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAP3K8, MCL1, MDM2, MDM4, MEN1, MERTK, MET, MITF, MLH1, MLL, MLL2, MLL3, MPL, MRE11A, MSH2, MSH6, MTF2, MTHFR, MTOR, MTUS2, MYC, MYCL1, MYCN, MYD88, NAT2, NF1, NF2, NFE2L2, NKX2-1, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NPM1, NQO1, NRAS, NTRK1, NTRK2, NTRK3, PAK7, PAX5, PBRM1, PDGFRA, PDGFRB, PDPK1, PHF6, PHF19, PIK3CA, PIK3CD, PIK3R1, PIM1, PLK1, PRKDC, PTCH1, PTEN, PTK2, PTK2B, PTPN11, PTPRD, RAF1, RB1, REL, RET, RICTOR, ROR2, ROS1, RPTOR, RRM1, RUNX1, RUNX1T1, SCN5A, SETD2, SETDB1, SLCO1B1, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMO, SOCS1, SPEN, SRC, STAT3, STK11, SUFU, SULT1A1, SUPT4H1, SUPT5H, TCF3, TCF4, TERT, TET1, TET2, TGFBR2, TMPRSS2, TNFAIP3, TNK2, TOP1, TOP2A, TP53, TPMT, TSC1, TSC2, TSHR, TYK2, TYMS, UGT1A1, UTY, VHL, VKORC1, WHSC2, WT1, ZNF668 |
(98) |
| 15 | Anorectal melanoma; United States (somatic) | 14/15 (93%) | 467 ABL1, AKT1, AKT2, AKT3, ALK, ALOX12B, AMER1, APC, AR, ARAF, ARID1A, ARID1B, ARID2, ARID5B, ASXL1, ASXL2, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXIN2, AXL, B2M, BAP1, BARD1, BBC3, BCL2L1, BCL2L11, BCL6, BCL11B, BCOR, BCORL1, BCR, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRCC3, BRD3, BRD4, BRIP1, BTK, BUB1B, CALR, CARD11, CASP8, CBL, CBLB, CBLC, CCND3, CCNE1, CD58, CD74, CD79A, CD79B, CD274, CD276, CDC6, CDC7, CDC45, CDC73, CDCA5, CDH1, CDK4, CDK6, CDK8, CDK12, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CDT1, CEBPA, CHEK1, CHEK2, CIC, CIITA, CLTC, CLTCL1, CNOT3, CREBBP, CREBBP, CRKL, CRLF2, CRLF2, CSF1R, CSF3R, CTCF, CTLA4, CTNNB1, CUL3, CYLD, DAXX, DCUN1D1, DDB2, DDR2, DICER1, DIS3, DNM2, DNMT1, DNMT3A, DNMT3B, DOT1L, E2F3, ECT2L, EED, EGFL7, EGFR, EIF1AX, EP300, EPCAM, EPHA3, EPHA5, EPHB1, ERBB2, ERBB3, ERBB4, ERCC2, ERCC3, ERCC4, ERCC5, ERG, ESR1, ETV1, ETV4, ETV5, ETV6, EWSR1, EXT1, EXT2, EZH2, EZR, FAM46C, FAM175A, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FAS, FAT1, FBXO11, FBXW7, FGF3, FGF4, FGF19, FGFR1, FGFR2, FGFR3, FGFR4, FH, FIP1L1, FLCN, FLT1, FLT3, FLT4, FOXA1, FOXL2, FOXO1, FUBP1, FUS, FYN, GATA1, GATA2, GATA3, GMNN, GNA11, GNA13, GNAQ, GNAS, GNB1, GOPC, GPC3, GREM1, GRID1, GRIN2A, GSK3B, H3F3A, H3F3C, HGF, HIST1H1C, HIST1H2BD, HIST1H3B, HMGA2, HNF1A, HRAS, ICOSLG, ID3, IDH1, IDH2, IFNGR1, IGF1, IGF1R, IGF2, IKBKE, IL2, IL6ST, IL7R, IL10, INPP4A, INPP4B, INSR, IRF1, IRF4, IRF8, IRS1, IRS2, ITK, JAK1, JAK2, JAK3, JUN, KAT6A, KCNJ5, KDM5C, KDM6A, KDM6B, KDR, KEAP1, KIAA1549, KIF5B, KIT, KLF4, KLF6, KLHL6, KMT2A, KMT2C, KMT2D, KRAS, LAMB4, LATS1, LATS2, LMO1, LRIG3, LUC7L2, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAP3K13, MAPK1, MAX, MCL1, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDC1, MDM2, MDM4, MECOM, MED12, MEF2B, MEN1, MET, MITF, MLH1, MLLT10, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYC, MYCL, MYCN, MYD88, MYOD1, NBN, NCOR1, NF1, NF2, NFE2L2, NIPBL, NKX2-1, NKX3-1, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NPM1, NRAS, NT5C2, NTRK1, NTRK2, NTRK3, NUP98, NUP214, NUTM1, PAK1, PAK7, PALB2, PARK2, PARP1, PAX5, PAX8, PBRM1, PDCD1, PDGFRA, PDGFRB, PDPK1, PHF6, PHF8, PHOX2B, PICALM, PIGA, PIK3C2G, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PLAG1, PLK2, PMAIP1, PML, PMS1, PMS2, PNRC1, POLE, POT1, PPARG, PPP2R1A, PRDM1, PRF1, PRKAR1A, PRPF8, PRPF40B, PTCH1, PTEN, PTPN1, PTPN11, PTPRC, PTPRD, PTPRS, PTPRT, PTTG1, RAC1, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD52, RAD54L, RAF1, RARA, RASA1, RB1, RBM10, RECQL4, REL, RET, RFWD2, RHOA, RICTOR, RIT1, RNF43, ROS1, RPL5, RPL10, RPS6KA4, RPS6KB2, RPTOR, RUNX1, RYBP, SBDS, SDHA, SDHAF2, SDHB, SDHC, SDHD, SETBP1, SETD2, SF1, SF3A1, SF3B1, SH2B3, SH2D1A, SHQ1, SLC45A3, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMARCD1, SMARCE1, SMC1A, SMC3, SMO, SOCS1, SOX2, SOX9, SOX17, SPEN, SPOP, SRC, SRSF2, SS18, SSX1, SSX2, SSX4, STAG1, STAG2, STAG3, STAT3, STAT5B, STAT6, STK11, STK40, SUFU, SUZ12, SYK, TAF15, TBL1XR1, TBX3, TCF3, TCF12, TERT, TET1, TET2, TET3, TFE3, TGFBR1, TGFBR2, TMEM127, TMPRSS2, TNFAIP3, TNFRSF14, TOPBP1, TP53, TP53BP1, TP63, TPM3, TRAF7, TSC1, TSC2, TSHR, U2AF1, U2AF2, UBR5, USP6, VHL, VTCN1, WAS, WRN, WT1, XIAP, XPA, XPC, XPO1, YAP1, YES1, ZRSR2 |
(99) |
| 451 families | Patients with cutaneous and uveal melanomas who had family history of melanoma, but no CDKN2A or CDK4 mutations; Netherlands (germline) |
18/451 (4%) | 30 ACD, BAP1, BRIP1, CBLB, CDK4, CDKN2A, CENPS, CREB3L1, DOT1L, ERCC3, MC1R, MITF, MLLT6, NEK10, NEK11, NEK2, NEK4, OCA2, PARP1, POLE, POLH, POT1, PTEN, RAD51B, RASEF, TERF1, TERF2IP, TERF2IP, TERT, TINF2 |
(100) |
| 264 | High risk melanoma patients with family history, other cancers, multiple primary melanomas, or early onset; Czech Republic (germline analysis of peripheral blood) |
43/264 (16%) | 217 ABLIM1, ACD, AGR3, APC, APEX1, ARNT, ASIP, ATM, ATRN, AURKA, BAP1, BARD1, BBC3, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, BRMS1, CASP8, CASP10, CBL, CCAR2, CCND1, CCNH, CDH1, CDK4, CDK7, CDK10, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CEBPA, CHEK2, CLPTM1L, COX8A, CTLA4, CTNNB1, CYP1A1, CYP1A2, CYP3A5, CYP11A1, CYP17A1, CYP19A1, DAB2IP, DCAF4, DDB1, DDB2, EDNRB, EGF, EGFR, EIF1AX, EPCAM, ERBB2, ERBB4, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERCC6, ERCC8, EXOC2, EZH2, FANCC, FANCL, FANCM, FAS, FASLG, FGFR2, FGFR4, FH, FLCN, FLT1, FOXP3, FTO, GATA2, GATA4, GC, GNA11, GNAQ, GPC3, GSTM1, GSTM3, GSTP1, GSTT1, H2AFY, HERC2, HRAS, IDH1, IDH2, IFIH1, IFNA1, IFNG, IL2RA, IL4, IL6, IL8, IL10, ING4, IRF4, KAT6A, KIAA1967, KIT, KMT2A, KRAS, LRIG1, MAP2K1, MC1R, MDM2, MET, MGMT, MITF, MLH1, MLH3, MMP1, MMP3, MSH2, MSH3, MSH6, MTAP, MUTYH, MX2, MYH7B, NBN, NCOA6, NF1, NF2, NFKB1, NFKBIE, NOD2, NOTCH3, NRAS, OBFC1, OCA2, PALB2, PARP1, PAX5, PDGFRA, PIGU, PIK3CA, PIK3R1, PIK3R4, PLA2G6, PMAIP1, PMS1, PMS2, POLD1, POLE, POLH, POMC, POT1, PPM1D, PPP6C, PRF1, PTCH1, PTEN, PTGS2, PTPN11, PTPN22, RAC1, RAD23A, RAD23B, RAD51C, RAD51D, RASEF, RB1, RECQL, RECQL4, RET, RHOBTB2, RUNX1, SBDS, SDHA, SDHB, SDHC, SDHD, SETDB1, SF3B1, SH2B3, SLC24A4, SLC45A2, SLX4, SMAD4, SMARCB1, SNX31, STAG2, STK11, STK19, SUZ12, TACC1, TERC, TERF1, TERF2, TERF2IP, TERT, TINF2, TLR3, TP53, TRPM1, TSC1, TSC2, TYR, TYRP1, VDR, VHL, WRN, WT1, XAB2, XPA, XPC, XRCC1, XRCC3, ZNF365 |
(101) |
| 102 | Melanoma patients with multiple primary melanomas; Italy (germline analysis of peripheral blood) |
76/102 (75%) | 29 ACD, AGR3, ARNT, ASIP, ATM, BAP1, CASP8, CCND1, CDK4, CDKAL1, CDKN2A, FTO, GC, IRF4, MC1R, MITF, MX2, OBFC1, OCA2, PALB2, PARP1, POT1, RMND2, SLC45A2, TERF21P, TERT, TMEM38B, TYR, TYRP1 |
(102) |
Bolded: Top three mutated genes.