Chromosomal abnormalities identified in T-ALL by SNP array analysis
| Cases . | Gain/loss . | Chromosome . | Cytogenetic location . | Size, Mb . | No. of genes . | Candidate genes . |
|---|---|---|---|---|---|---|
| VIIId,r | Loss | 1 | p21.1-31.1 | 28 | >50 | LMO4 |
| VIIId,r | Loss | 1 | p13.1-2 | 2.8 | 30 | |
| IIIr | Loss | 1 | q32.3-44 | 35 | >50 | WNT9A |
| IVd | Loss | 2 | q21.1-31.2 | 20 | >50 | TANK |
| IVd | Loss | 3 | q12.1-21.3 | 34 | >50 | mir-198 |
| VIIIr | Loss | 3 | q26.3-27.1 | 8.6 | 50 | SOX2 |
| IXd | Loss | 4 | q21.1 | 0.06 | 0 | |
| IIId, IVd | Loss | 4 | q31.2-31.3* | 1 | 5 | FBXW7 |
| IVd, IXd | Loss | 5 | q23.3-32* | 16 | >50 | CTNNA1 |
| Id, VIr, VIId,r | Loss | 6 | q13-16.3* | 27 | >50 | |
| VIIId | Gain | 6 | q15-27 | 84 | >50 | |
| VIIIr | Loss | 7 | p11.2-12.3 | 7.5 | 20 | IKZF1 |
| VIIIr | Loss | 7 | p21.3 | 1.6 | 3 | |
| VIIIr | Loss | 7 | q31.3 | 0.8 | 4 | |
| VIIId | Gain | 8 | p11.2-23 | 43 | >50 | |
| IId,r; IIId,r; Vd,r; VId,r; VIId,r; VIIId,r | Loss | 9 | p21.3* | 0.16 | 2 | p16/INK4A; p14/ARF |
| Vd,r | Gain | 9 | q34.12 | 0.6 | 2 | NUP214-ABL1 |
| Vd,r | Loss | 9 | q34.13 | 0.5 | 6 | |
| VIIId,r | Gain | 9 | q22.2-34.3 | 39 | >50 | |
| IVd | Loss | 10 | q26.2 | 1.5 | 1 | MGMT |
| Vd,r | Loss | 11 | p13-14.1 | 2.8 | 18 | WT1, PAX6 |
| Id, IVd, IXd | Loss | 12 | p12.3-13.31* | 10 | >50 | ETV6, CDKN1B, BCL2L14 |
| Id | Gain | 14 | q13.1-21.3 | 25 | >50 | |
| Id; VIIId,r | Loss | 14 | q23.1* | 1.5 | 10 | |
| Id; VIIId,r | Loss | 14 | q23.2* | 1.8 | 8 | |
| Id; VIIId,r | Loss | 14 | q24.4-24.3* | 6.3 | >50 | |
| Id; Vd,r; VIIId,r | Loss | 14 | q32.1* | 2.2 | 20 | |
| Vd,r | Loss | 14 | q32.2 | 1.1 | 6 | |
| IXd,r | Loss | 14 | q31.1-1.2 | 1 | 3 | BCL11B |
| IXd,r | Gain | 14 | q32.1-3 | 17 | >50 | TRAF3, DICER1 |
| IXd,r | Gain | 22 | q12.3-13.3 | 48.5 | >50 | WNT7B, CERK |
| VId,r | Loss | 22 | q11.2 | 0.2 | 1 | VPREB1 |
| Cases . | Gain/loss . | Chromosome . | Cytogenetic location . | Size, Mb . | No. of genes . | Candidate genes . |
|---|---|---|---|---|---|---|
| VIIId,r | Loss | 1 | p21.1-31.1 | 28 | >50 | LMO4 |
| VIIId,r | Loss | 1 | p13.1-2 | 2.8 | 30 | |
| IIIr | Loss | 1 | q32.3-44 | 35 | >50 | WNT9A |
| IVd | Loss | 2 | q21.1-31.2 | 20 | >50 | TANK |
| IVd | Loss | 3 | q12.1-21.3 | 34 | >50 | mir-198 |
| VIIIr | Loss | 3 | q26.3-27.1 | 8.6 | 50 | SOX2 |
| IXd | Loss | 4 | q21.1 | 0.06 | 0 | |
| IIId, IVd | Loss | 4 | q31.2-31.3* | 1 | 5 | FBXW7 |
| IVd, IXd | Loss | 5 | q23.3-32* | 16 | >50 | CTNNA1 |
| Id, VIr, VIId,r | Loss | 6 | q13-16.3* | 27 | >50 | |
| VIIId | Gain | 6 | q15-27 | 84 | >50 | |
| VIIIr | Loss | 7 | p11.2-12.3 | 7.5 | 20 | IKZF1 |
| VIIIr | Loss | 7 | p21.3 | 1.6 | 3 | |
| VIIIr | Loss | 7 | q31.3 | 0.8 | 4 | |
| VIIId | Gain | 8 | p11.2-23 | 43 | >50 | |
| IId,r; IIId,r; Vd,r; VId,r; VIId,r; VIIId,r | Loss | 9 | p21.3* | 0.16 | 2 | p16/INK4A; p14/ARF |
| Vd,r | Gain | 9 | q34.12 | 0.6 | 2 | NUP214-ABL1 |
| Vd,r | Loss | 9 | q34.13 | 0.5 | 6 | |
| VIIId,r | Gain | 9 | q22.2-34.3 | 39 | >50 | |
| IVd | Loss | 10 | q26.2 | 1.5 | 1 | MGMT |
| Vd,r | Loss | 11 | p13-14.1 | 2.8 | 18 | WT1, PAX6 |
| Id, IVd, IXd | Loss | 12 | p12.3-13.31* | 10 | >50 | ETV6, CDKN1B, BCL2L14 |
| Id | Gain | 14 | q13.1-21.3 | 25 | >50 | |
| Id; VIIId,r | Loss | 14 | q23.1* | 1.5 | 10 | |
| Id; VIIId,r | Loss | 14 | q23.2* | 1.8 | 8 | |
| Id; VIIId,r | Loss | 14 | q24.4-24.3* | 6.3 | >50 | |
| Id; Vd,r; VIIId,r | Loss | 14 | q32.1* | 2.2 | 20 | |
| Vd,r | Loss | 14 | q32.2 | 1.1 | 6 | |
| IXd,r | Loss | 14 | q31.1-1.2 | 1 | 3 | BCL11B |
| IXd,r | Gain | 14 | q32.1-3 | 17 | >50 | TRAF3, DICER1 |
| IXd,r | Gain | 22 | q12.3-13.3 | 48.5 | >50 | WNT7B, CERK |
| VId,r | Loss | 22 | q11.2 | 0.2 | 1 | VPREB1 |
d indicates diagnostic samples; and r, relapse samples.
Common minimally deleted regions are indicated.