TABLE 1.
Results of the targeted sequencing from the paired samples of 72 patients
| No(UPN) | Diagnosis | Kary otype | leukaemia‐free survival (m) | Presumed last event | All gene mutations |
|---|---|---|---|---|---|
| The patients in whom AML transformation‐related mutations could be presumed by paired sequencing analysis (listed as signalling pathway activation, transcription factors and tumour suppressors signalling pathway activation | |||||
| 1.(809) | RCMD | normal |
CEBPA/1/K352fs(15) FLT3/9/D358V(48) RUNX1/6/508 + 1G > C(24)/5/G170R(23) |
ASXL1; CEBPA; EZH2; FLT3; RUNX1*2; STAG2; TET2 | |
| AML | normal | 17 |
FLT3/9/D358V(48) RUNX1/6/508 + 1G > C(45)/5/G170R(42) NRAS/2/G13R(48) |
ASXL1; EZH2; FLT3; RUNX1 × 2; STAG2; TET2; BCOR; NRAS | |
| 2.(1057) | RAEB1 | normal | PTPRD/10/A539V(51) | DNMT3A; PTPRD; STAG2; U2AF1 | |
| AML | normal | 48 |
PTPRD/10/A539V(46) RUNX1/4/L98fs(28) NRAS/2/3/G12V/Q61L(15) (15) CBL/8/C384R(12) |
DNMT3A; PTPRD; STAG2; U2AF1; CBL; NRAS×2; RUNX1 | |
| 3.(2356) | RAEB1 | normal |
PHF6/4/C107fs(16) RUNX1/5/A149_A150delinsGX(16) TP53/3/c.74 + 14 T > C(51) |
BCOR; ITIH3; PHF6; RUNX1; TET2; TP53 | |
| AML | normal | 6 |
PHF6/4/C107fs(23) RUNX1/5/A149_A150delinsGX(21) TP53/3/c.74 + 14 T > C(55) KRAS/2/G13D(25) |
BCOR; ITIH3; PHF6; RUNX1; TET2; TP53; EZH2; KRAS | |
| 4.(2998) | RAEB2 | normal |
RUNX1/9/967 + 1 > A6/886 + 1 > A(31) KRAS/2/G12S(30) |
ASXL1; KRAS; RUNX1; U2AF1 | |
| AML | normal | 2 |
RUNX1/9/967 + 1 > A6/886 + 1 > A(28) KRAS/2/G12S(27) |
ASXL1; KRAS; RUNX1; U2AF1 | |
| 5.(2747) | RAEB2 | normal | BCOR; ITIH3 | ||
| AML | normal | 10 | NRAS/2/G12D(57) | BCOR; ITIH3; KIF20B; NRAS; STAG2; | |
| 6.(3430) | CMML1 | normal |
GATA2/4/G327E(29)/4/323_323del(13) RUNX1/6/D198Y(41) KRAS/2/G12C(11) NRAS/2/G12D(29) |
GATA2*2; KRAS; NRAS; RUNX1; SF3B1; UPF3A | |
| AML | normal | 7 |
GATA2/4/G327E(29)/4/323_323del(38) RUNX1/6/D198Y(43) KRAS/2/G12C(45) |
GATA2*2; KRAS; RUNX1; SF3B1; UPF3A; EZH2 | |
| 7.(3435) | RCMD | normal | RUNX1/1/P86S(46) | ASXL1; EZH2; RUNX1; STAG2; UPF3A | |
| AML | normal | 33 |
RUNX1/1/P86S(43) PTPN11/3/F71L(34) NRAS/2/G12D(9.7) |
ASXL1; EZH2; RUNX1; STAG2; UPF3A; BCOR; NRAS; PTPN11 | |
| 8.(3541) | RAEB2 | del20q‐ | GATA2/5/L345W(43) | DNMT3A; GATA2; TET2 | |
| AML | del20q‐ | 14 |
GATA2/5/L345W(30) KRAS/2/G12R(30) |
DNMT3A; GATA2; TET2; BCOR; KRAS | |
| 9.(3626) | RCMD | normal | ASXL1; DHX9; IDH1; RUNX1; TET2; U2AF1 | ||
| AML | NA | 29 |
ETV6/6/G381fs(48) NRAS/2/G12A(44) |
ASXL1; DHX9; IDH1; RUNX1; TET2; U2AF1; ETV6; NRAS | |
| 10.(4674) | RCMD | Complex |
RUNX1/1/H78Y(53) ETV6/6/R339I(15) |
DNMT3A; ETV6; EZH2; KIF20B; RUNX1; SETBP1 | |
| AML | Complex | 5 |
RUNX1/1/H78Y(43) NRAS/2/G12A(23) PTPN11/3/A72V(18) |
DNMT3A; KIF20B; RUNX1; SETBP1; NRAS; PTPN11; | |
| 11.(4687) | RCMD | normal |
GATA2/3/M223I(51) RUNX1/2/G138fs(42) |
ASXL1; EZH2; GATA2; RUNX1; STAG2; TET2*2 | |
| AML | NA | 6 |
GATA2/3/M223I(55) RUNX1/2/G138fs(50) NRAS/2/G12D(52) |
ASXL1; EZH2; GATA2; RUNX1; STAG2; TET2*2; ROBO1; NRAS | |
| 12.(4877) | RCMD | normal |
MPL/2/A58V(47) KRAS/2/G12S(41) |
ASXL1; KRAS; MPL; STAG2; TET2; | |
| AML | normal | 17 |
MPL/2/A58V(46) KRAS/2/G12S(55) PTPRD/23/R588C(52) |
ASXL1; KRAS; MPL; STAG2; TET2; PTPRD | |
| 13.(5305) | RCMD | normal | NRAS/2/G13D(4.1)/2/G12D(3.4) | IDH1; KMT2D; NRAS; | |
| AML | normal | 9 |
NRAS/2/G13D(38) ETV6/4/H141Tfs313(16) |
IDH2; KMT2D; NRAS; ETV6 | |
| 14.(5253) | RCMD | normal | None | None | |
| AML | t(3; 6), −7 | 40 |
RUNX1/6/R201Q(48) NRAS/3/Q61H(25) PTPN11/3/E69K(23.4) |
ANKRD11; NRAS; PTPN11/RUNX1 | |
| 15.(1587) | RAEB1 | der2 |
JAK2/14/V617F(46) FLT3/19/c.2208‐14A.G(52) |
IDH2; FLT3; JAK2; U2AF1; ZRSR2 | |
| AML | der2 | 25 |
JAK2/14/V617F(43) FLT3/19/c.2208‐14A.G(49) |
IDH2; FLT3; JAK2; U2AF1; ZRSR2 | |
| 16.(1792) | RAEB1 | der4 | RUNX1/9/Q397R(47) | RUNX1; U2AF1 | |
| AML | der4 | 8 |
RUNX1/9/Q397R(30) FLT3/11/E444V(37)11/E444X(37) |
RUNX1; U2AF1; FLT3*2; ROBO1; | |
| 17.(2117) | RCMD | complex | TP53/5/8/Y126C(16)/R273S(15) | SRSF2; TP53*2 | |
| AML | complex | 8 |
TP53/5/8/Y126C(14)/R273S(14) FLT3/9/D358V(55) |
TP53*2; FLT3 | |
| 18.(2570) | RAEB1 | normal | RUNX2/6/D198N(35) | IDH2; RUNX1; SRSF2 | |
| AML | +8 | 5 | FLT3/11/A445V(49)/11/A445S(49) | FLT3*2; | |
| 19.(2577) | CMML1 | normal |
CEBPA/1/p69‐70del(17) NPM1/10/L258fs(33) |
CEBPA; DNMT3A; NPM1; ROBO1; TET2 | |
| AML | normal | 11 |
CEBPA/1/p69‐70del(21) NPM1/10/L258fs(25) FLT3/14/K602delinsREYEYDLK (14) |
CEBPA; DNMT3A; NPM1; ROBO1; TET2; FLT3 | |
| 20.(3183) | RCMD | add (3) + 8 | BCOR; DHX9; EZH2*2; IDH1; ROBO1; STAG2; U2AF1 | ||
| AML | add (3) + 8 | 6 |
FLT3/9/D358V(52) CBL/11/C1564‐13C > T(40) |
BCOR; DHX9; EZH2*2; IDH1; ROBO1; STAG2; U2AF1; CBL; FLT3; TET2 |
|
| 21.(4383) | RCMD | normal | DNMT3A; SF3B1 | ||
| AML | +1, der(1; 16) | 18 |
PHF6/2/S22★(5.6) FLT3/9/T382M(45) CBL/15/E765G(49) KIT/14/S713F(49) |
DNMT3A; SF3B1; CBL; FLT3; KIT; PHF6 | |
| 22.(5135) | RAEB2 | Add7, del20q | ASXL1; ITIH3; TET2; U2AF1 | ||
| AML | Add7, del20q | 5 | FLT3‐ITD(high)1.597 | ASXL1; ITIH3; TET2; U2AF1; FLT3‐ITD | |
| 23.(692) | CMML2 | normal |
GATA2/3/S186T(47) PHF6/9/:c.968 + 1G > A(25) RUNX1/9/F416fs(27) |
GATA2; ITIH3; PHF6; RUNX1; SF3B1; | |
| AML | normal | 10 |
GATA2/3/S186T(50) PHF6/9/:c.968 + 1G > A(26) RUNX1/9/F416fs(24) CBL/9/R420Q(34) |
GATA2; ITIH3; PHF6; RUNX1; SF3B1; CBL | |
| 24.(1891) | CMML1 | der22 | DNMT3A; ROBO2; TET2 | ||
| AML | der22 | 14 |
CBL/11/c.1564‐13C > T(56) CEBPA/1/A265fs(37)K90fs(52) |
DNMT3A; ROBO2; TET2*2; CBL; CEBPA*2; EZH2 | |
| 25. (2206) | RCMD | +8 |
NF1/17/M645V(49) PTPRD/29A1047S(44) CBL/8/C396R(27) |
ANKRD11; ASXL1; CBL; NF1; PTPRD; U2AF1 | |
| AML | +8 | 3 |
NF1/17/M645V(51) PTPRD/29A1047S(40) CBL/8/C396R(21) |
ANKRD11; ASXL1; CBL; NF1; PTPRD; U2AF1 | |
| 26.(4559) | RAEB2 | complex | CBL/15/S791fs(9.6)/15/L790fs(9.7) | ANKRD11; ASXL1; CBL*2; ROBO1 | |
| AML | complex | 11 | CBL/15/S791fs(8.7)/15/L790fs(8.8) | ANKRD11; ASXL1; CBL*2; ROBO1 | |
| 27.(2638) | CMML1 | normal | PTPN11/14/P563R(43) | PTPN11; ROBO1; | |
| AML | normal | 16 | PTPN11/14//P563R(45) /3/D61V(37) | PTPN11 × 2; ROBO1; SF3B1 | |
| 28.(4133) | RAEB1 | complex |
CBL/9/R420Q(71) TP53/4/c.306‐2A > G(96) |
ASXL1; CBL; ROBO2; TP53 | |
| AML | complex | 3 |
CBL/9/R420Q(39) TP53/4/c.306‐2A > G(97) PTPN11/13/G507V(28) |
ASXL1; CBL; ROBO2; TP53; PTPN11 | |
| 29.(4410) | RAEB1 | del20q | PTPN11/3/D61H(33) | EZH2; PTPN11; SETBP1; TET2 | |
| AML | del20q | 12 | PTPN11/3/D61H(48) | EZH2; PTPN11; SETBP1; TET2 | |
| 30.(4820) | RCMD | Add3, add18 | EZH2; KMT2D; U2AF1 | ||
| AML | Add3 | 15 | PTPN11/3/E76A(8.0) | EZH2; KMT2D; U2AF1; PTPN11 | |
| 31.(3891) | RCMD | normal | PTPRD/18/I930V(51) | ASXL1; PTPRD | |
| AML | normal | 8 | PTPRD/18/I930V(46) | ASXL1; PTPRD | |
| 32.(702) | RCMD | der16, (1; 16) del20q | ANKRD11; SRSF2 | ||
| AML | der16t (1; 16) del20q | 28 |
MPL/10/W515L(17) GATA2/6/R396W(15) |
ANKRD11; SRSF2; GATA2; IDH1; MPL | |
| Myeloid transcriptors | |||||
| 33.(1018) | RAEB2 | derX, der14 | DNMT3A; EZH2; TET2 | ||
| AML | derX, der14 | 4 |
FLT3:/9/D358V(53) CEBPA/1/A295V(39) |
DNMT3A; EZH2; TET2; BCOR; CEBPA; FLT3 | |
| 34.(1090) | RARS | del20q | RUNX1/9/D344G(45) | DNMT3A; DHX9; RUNX1; SRSF2; | |
| AML | del20q | 11 |
RUNX1/9/D344G(48)/7/R232W(20) CEBPA/1/Y285fs(32) |
DNMT3A; DHX9; RUNX1*2; SRSF2; ASXL1; CEBPA; SETBP1 | |
| 35.(1243) | RCMD | normal | ASXL1; U2AF1 | ||
| AML | normal | 18 | CEBPA/1/7_15del(40) | ASXL1; U2AF1; CEBPA; IDH1 | |
| 36 (1931) | RAEB1 | complex | CEBPA/1/S9F(67) | CEBPA; DNMT3A; TET2; U2AF1 | |
| AML | complex | 9 | CEBPA/1/S9F(46) | CEBPA; DNMT3A; TET2; U2AF1 | |
| 37.(3288) | RN | normal | KIF20B; STAG2; TET2*2 | ||
| AML | normal | 12 | CEBPA/1/L338P(36) | KIF20B; STAG2; TET2*2; ASXL1; CEBPA; EZH2 | |
| 38.(3552) | RARS | ‐Y | SF3B1; TET2 | ||
| AML | NA | 28 | CEBPA/1/c238delineCSG(18) | SF3B1; TET2; CEBPA; IDH2; SRSF2; STAG2 | |
| 39.(3826) | RCMD | del7 | ASXL1; EZH2 | ||
| AML | normal | 22 | CEBPA/1/Y166X(48)P58fs(47) | ASXL1; EZH2; CEBPA*2 | |
| 40.(4196) | RCMD | del20q, +21 |
PHF6/4/G93S(27) RUNX1/1/R80C(51) |
PHF6; RUNX1; SRSF2; | |
| AML | del20q, +21 | 8 |
PHF6/4/G93S(45) RUNX1/1/R80C(78) NRAS/2/G12D(34) CEBPA/1/69_70del(11) |
PHF6; RUNX1; SRSF2; CEBPA; NRAS | |
| 41.(4634) | RAEB2 | normal |
NPM1/7/L160fs(24) NRAS/2/G13D(16) |
NPM1; NRAS; SF3B1; TET2 | |
| AML | normal | 2 |
NPM1/7/L160fs(35) NRAS/2/G13D(37) CEBPA/1/69_70del(9.8) |
NPM1; NRAS; SF3B1; TET; CEBPA | |
| 42.(4806) | CMML1 | normal | ANKRD11; DHX9; TET2; | ||
| AML | +8 | 11 | CEBPA/1/1/E228fs(4.8)/L212Q(28) | ANKRD11; DHX9; TET2; CEBPAX2 | |
| 43.(1350) | RAEB1 | complex |
PHF6/9/Y303X(56) RUNX1/9/P333fs(29) |
EZH2; PHF6; RUNX1; TET2 | |
| AML | complex | 2 |
PHF6/9/Y303X(46) RUNX1/9/P333fs(17) |
EZH2; PHF6; RUNX1; TET2 | |
| 44.(1582) | CMML1 | normal | PTPRD/22/c.962‐9C > G(47) | KIF20B; PTPRD; SF3BA; TET2 | |
| AML | normal | 13 |
PTPRD/22/c.962‐9C > G(43) RUNX1/9/P340fs(40) |
KIF20B; PTPRD; SF3BA; TET2; RUNX1 | |
| 45.(3479) | RCMD | normal | RUNX1/3/R174Q(28) | ASXL1; RUNX1; TET2; ZRSR2 | |
| AML | normal | 15 | RUNX1/3/R174Q(42) | ASXL1; RUNX1; TET2*2; ZRSR2 | |
| 46.(3536) | RCMD‐RS | normal | RUNX1/4/H105Y(40) | ASXL1; ROBO1; RUNX1; SF3B1; UPF3A | |
| AML | del5q | 3 | RUNX1/4/H105Y(34) | ASXL1; ROBO1; RUNX1; SF3B1; UPF3A | |
| 47.(4143) | RAEB1 | normal | RUNX1/4/S229fs(34) | BCOR; DNMT3A; IDH2; ROBO1; RUNX1 | |
| AML | normal | 3 | RUNX1/4/S229fs(39) | BCOR; DNMT3A; IDH2; ROBO1; RUNX1 | |
| 48.(811) | RCMD | der6, t (1;6) | None | ||
| AML | der6, t (1;6) | 26 |
ETV6/6/V345L(52) MPL/10/W515R(50) |
ETV6; MPL | |
| 49.(4390) | RCMD | normal |
ETV6/7/M389R(33) PHF6/10/R342X(27) |
ASXL1; BCOR; ETV6; PHF6 | |
| AML | inv3add3 | 15 |
PHF6/10/R342X(45) ETV6/7/M389R(42) |
BCOR; ETV6; PHF6 | |
| 50.(1601) | RAEB2 | normal | SETBP1/3/c487‐3C > T(44) | SETBP1 | |
| AML | normal | 8 | SETBP1/3/c487‐3C > T(43) | SETBP1 | |
| 51.(3053) | RAEB2 | normal | STAG2; UPF3A | ||
| AML | normal | 40 | SETBP1/4/D868N(18) | SETBP1; SRSF2 | |
| Tumour suppressors | |||||
| 52.(843) | RCMD | der1del1 | SRSF2; TET2 | ||
| AML | der1 | 3 | TP53/5/C135X(18) | SRSF2; TET2; TP53 | |
| 53.(1354) | RAEB1 | normal | None | ||
| AML | complex | 7 | TP53/8/E287fs(40)/6/G199E(28) | ASXL1; TP53 × 2 | |
| 54.(1445) | RAEB2 | normal | TP53/8/E287D(56) | ROBO1; TP53; UPF3A | |
| AML | del11q | 27 | TP53/8/E287D(48) | ROBO1; TP53; UPF3A | |
| 55.(1694) | RAEB2 | complex | TP53/7/M237I(74) | DNMT3A; TP53 | |
| AML | complex | 3 | TP53/7/M237I(80) | DNMT3A; TP53 | |
| 56.(1831) | RAEB1 | complex | TP53/4/W91X(30) | ANKRD11; DNMT3A; TP53 | |
| AML | complex | 13 | TP53/4/W91X(30)/5/R158L(31) | ANKRD11; DNMT3A; TP53*2; KIF20B; STAG2 | |
| 57.(2296) | RAEB2 | normal | DHX9; ROBO1 | ||
| AML | normal | 4.5 | TP53/9/R303fs(85) | DHX9; ROBO1; TP53 | |
| 58.(2666) | RAEB1 | normal | PTPRD/27/G809V(56) | DNMT3A; IDH2; PTPRD | |
| AML | normal | 18 |
PTPRD/27/G809V(51) TP53/5/P151S(25) |
DNMT3A; IDH2; PTPRD; TP53 | |
| 59.(3678) | RAEB1 | complex | TP53/5/530‐535del (34) | TP53 | |
| AML | complex | 15 | TP53/5/530‐535del(53) | TP53 | |
| 60.(3380) | CMML1 | complex | TP53/2/S83G(84) | TP53 | |
| AML | complex | 13 | TP53/2/S83G(60) | TP53 | |
| 61.(1670) | RCMD | del18q |
GATA2/5/M388fs(41) TP53/2/E11Q(51) ETV6/5/V285M(49) WT1/1/A115fs(12) |
BCOR; ETV6; GATA2; TET2; TP53; U2AF1; WT1 | |
| AML | del18q | 2 |
GATA2/5/M388fs(40) TP53/2/E11Q(50) ETV6/5/V285M(53) WT1/1/A115fs(25) |
BCOR; ETV6; GATA2; TET2; TP53; U2AF1; WT1 | |
| 62.(1849) | RCMD | normal | WT1/7/H428fs(31) | DNMT3A; IDH1; TET2; WT1 | |
| AML | normal | 8 | WT1/7/H428fs(40) | DNMT3A; IDH1; TET2*2; WT1 | |
| 63.(3567) | RAEB2 | normal |
FLT3/12/c.1419–3‐ > T(15) NPM1/10/R262fs(43)/10W259delinsWQ(44)/10/R262S(44)/7/W163L(42) |
DHX9; DNMT3A; ANKRD11; FLT3; NPM*4 | |
| AML | normal | 4 |
NPM1/10/R262fs(12)/10W259delinsWQ(25)/10/R262S(19)/7/W163L(20) WT1/7/S169fs(32) |
DHX9; DNMT3A; ANKRD11; NPM×4; ROBO1; WT1 | |
| 64.(1892) | RAEB2 | normal | NPM1/11/L287f(35) | DNMT3A; IDH1; NPM1 | |
| AML | normal | 9 | NPM1/11/L287f(31) | DNMT3A; IDH1; NPM1 | |
| The patients in whom last gene events could not be presumed by paired targeted sequencing analysis | |||||
| 65.(1075) | RA | normal | DHX9; IDH2; ROBO2; STAG2; UPF3A | ||
| AML | normal | 20 | DHX9; IDH2; ROBO2; STAG2; UPF3A; TET2 | ||
| 66.(1619) | RAEB2 | complex | DHX9; DNMT3A; ITIH3*2 | ||
| AML | complex | 25 | DHX9; DNMT3A; ITIH3*2 | ||
| 67.(1702)★ | RAEB2 | normal | SRSF2 | ||
| AML | der12 | 19 | SRSF2 | ||
| 68.(3831) ★ | RAEB2 | normal | ANKRD11; IDH2 | ||
| AML | normal | 4 | ANKRD11; IDH2 | ||
| 69.(3155) ★ | RCMD | +14, del20q | ROBO1 | ||
| AML | normal | 7.5 | ROBO1 | ||
| 70.(3437) | RA | Inv9 | DNMT3A; ROBO1 | ||
| AML | Inv9 | 3 | DNMT3A; ROBO1 | ||
| 71.(4145) | RCMD | +1, der(1:7) | EZH2;IDH1 | ||
| AML | NA | 14 | ASXL1; TET2*2; ZRSR2 | ||
| 72.(4404) | RAEB1 | complex | SRSF2; TET2 | ||
| AML | complex | 18 | TET2 | ||
Note: 1. The fifth column indicates the possible last event mutations. The mutations listed in italic and bold font are considered the final presumed TRMs according to the definition in the Method section. 2. The paired targeted sequencing analysis from the last eight patients could not define the TRMs, so three (with star signals) of them agreed to WES to look for possible TRMs. For the explanation of mutation type, splicing site mutation was shown in nucleotide variation. 3. In column 5, NRAS/2/G13R(48) means exon2, VAF was 48%.
Abbreviations: AML, acute myeloid leukaemia; CMML1/2, chronic myelomonocytic leukaemia 1/2; NA means no available data; RA, refractory anaemia; RAEB‐1/2, refractory anaemia with excess blasts‐1/2; RARS, refractory anaemia with ring sideroblasts; RCMD, refractory cytopenias with multilineage dysplasia.