Table 1 Comparison of cytogenetic and genomic findings from nine patients with adverse-risk AML
Case | Karyotypea | Complex karyotype | Composite karyotype | No. of cytogenetic abnormalities | CNVsb | Chromosomal rearrangementsb | Gene fusions | SNVs | |
|---|---|---|---|---|---|---|---|---|---|
Total | NGS concordant | ||||||||
1 | 51, XY, +Y, +der(1;7)(q10;p10), +6, +8, +10 [10] | Yes | 5 | 5 | Gains: 1q, 6, 7p, 8, 10, Y | RUNX1, PTPN11, BCOR | |||
2 | 45, XX, -7 [17] / 45, X, t(X;8)(p21.2;q24.1), -7 [2] / 46, XX[1] | 2 | 2 | Losses: 7, BCOR | t(X;8)(p11.4;q24.13) linked to BCOR deletion; t(3;15)(p24.3;q14) | IDH2 | |||
3 | 43~45, X, -Y, t(1;5)(q21;p13), t(1;6)(q21;p25), -2, add(2)(p21), add(3)(q27), del(3)(q27), add(4)(p16), del(4)(q33), del(5)(q31), add(6)(p25), del(6)(q21), -7, add(7)(q36), del(7)(q22), -8, add(8)(q24.3), del(8)(?q23), +del(8)(q22), add(9)(p22), add(9)(q34), add(11)(p15), add(12)(p13), -16, add(16)(p13.3), -17, der(17)t(11;17)(q13;p13), add(18)(q23), der(19)t(11;19)(q13;q13.3), -21, add(22)(p11.2), +4mar [cp20] | Yes | Yes | 31 | 9 | Gains: 1p36.33-p35.1, 2p25.3-p22.3, 2p21-p11.2 (BCL11A), 3q26.32-q29, 8q12.1-q23.1 (RUNX1T1), 11q13.4-q25 (ETS1), 12p13.33-p13.2, 17q25.1-q25.3 (SRSF2), 19p13.3, 20q13.32-q13.33 Losses: 2q11.2-q31.3, 7q21.3-q36.2, 11p15.5-p13 (WT1), 16q13-q24.3 (CTCF), 17p13.3-p12 (TP53), 17q11.2-q24.3 (NF1), 19q13.42-q13.43, Yq11.221-q12 | t(1;5)(q42.3;q12.3); t(3;12) (q26.2;p13.2) linked to gene fusion; t(9;20)(q34.11;q13.12); der(Y)t(Y;3)(q11.221;q26.32) linked to 3q gain and Yq loss; chr4/7 rearrangements linked to 7q loss; chr2/3/8/11/12/16/17/ 19/22/X rearrangements linked to CNVs | ETV6-MECOM | TP53 |
4 | 48-49, XX, +6, +8, +9, t(12;17)(p13;q11.2), i(17)(q10), inv(18)(q11.2q21) [cp20] | Yes | Yes | 6 | 5 | Gains: 6, 8, 9 Losses: 17p13.3-p13.1 (TP53), 18q21.2 (SMAD4) | t(11;12;17)(p15.4;p13.3;q11.2) linked to gene fusion (Figure 1) | NUP98-KDM5A | ASXL1 |
5 | 46, XY, del(6)(q21q23), t(10;11)(p1?2;q21), inv(12)(q15q24.1), del(15)(q2?4) [cp19] / 46, XY [1] | Yes | Yes | 4 | 3 | Losses: ARPP21, BBX, 6q16.1-q22.31 (FOXO3), MACC1, 8p12-p11.21 (FGFR1), 8q11.21-q11.23, SH2B3, TBX3, MIR5009, SETD4 | t(10;11)(p12.3;q14.2) linked to gene fusion; t(7;18) linked to MACC1 del; chr12 rearrangements linked to SH2B3 and TBX3 deletions | PICALM-MLLT10; FIP1L1-PDGFRA (only in relapse) | |
6 | 46, XX, del(5)(q31), t(11;12)(p13;p13) [4] / 45, idem, -13 [5] / 46, XX [1] | Yes | 3 | 3 | Losses: FHIT, CDH18, 5q22.2q32 (APC), LACE1/FOXO3, 11p13 (WT1), 11p13-p12, 12p13.2-p12.3 (ETV6), 12p11.1, 12q12, 13, SLC47A1 | chr11/12/17 rearrangements linked to CNVs and gene fusion (Figure 1) | NUP98-BPTF | WT1, ETV6 | |
7 | 43~48, XY, +?Y, +?Y, der(5)t(5;17)(q1?3;q11.2), -7, +8, -12, -13, t(16;18)(q24;q23), +1~2mar [cp10] | Yes | Yes | 8 | 5 | Gains: 8, 13q12.11-q12.2 (FLT3) Losses: 1p36.12-p36.11 (RPL11), 1p35.3-p35.2, 1p22.1-p21.3, 2p13.3-p13.1, 2p12-p11.2, 2q32.2-q37.3 (SF3B1), 5q11.2-q35.3 (APC, NPM1), 7, 12p13.2-p12.1 (ETV6), 12p12.1-p11.21, 12q12-q24.13, TCF12, 16q21-q22.2 (CTCF), 16q22.3-q24.3, 17p13.3-p11.2 (TP53), 17q11.2-q12 (NF1), 18p11.31, 18q22.3-q23 | chr1 rearrangements linked to three segmental losses; chr2/5/8/12/13/16/17/18 rearrangements linked to other CNVs; inv(7)(q11.22q36.3) | TP53 | |
8 | 42-45, X, der(X)t(X;3)(q28;q21), der(1)t(1;17)(p35;q21), -3, -5, add(8)(q13), -9, add(11)(q13), add(12)(q24), i(13)(q10), del(16)(q23), -17, -18, -19, +idic(22)(p12), +2r, +mar1 [cp9] / 46, XX [1] | Yes | Yes | 14 | 6 | Gains: 3q13.33-q29, 8q (MYC), 13, 22 Losses: 3, 5q31.1, 5q31.2-q35.3 (NPM1), SMARCA2, 9p13.2-p11.2 (PAX5), 9q33.1-q33.3, 12p13.33-p11.23 (ETV6), 16q21-q24.3 (CTCF), 17p13.2-p11.2 (TP53), 17q11.2-q12 (NF1), 19p13.2-p13.12 (JUNB), BCOR, KDM6A | chr1/5/8/9/11/12/16/17/19 rearrangements linked to CNVs | TP53 | |
9 | 46, XX, t(1;14)(q21;q11.2) [20] | 1 | 1 | t(1;14)(q23.2;q12) linked to truncation of ATP1A2 | DNMT3A, FLT3, TET2 | ||||
