Recurrent DNA copy number alterations less than 3 Mb in size in pediatric T-ALL (n = 73)
| Localization . | Type of aberration . | Start clone . | End clone . | Size, Mb . | Candidate gene(s)†/miRNA‡ . | Frequency . | Minimally overlapping region,§ n (%) . | Minimally overlapping region,‖ n (%) . |
|---|---|---|---|---|---|---|---|---|
| 3q12.1 | loss | RP11-121C1 | RP11-201E8 | 0.46 | COL8A1 | 5/73 (7%) | ||
| 3q13.11-13.12 | loss | RP11-16N5 | RP11-25F15 | 2.70 | CBLB,*ALCAM | 4/73 (5%) | ||
| 5q31.1-31.2 | loss | RP1-186K10 | CTB-46B19 | 1.52 | CTNNA1, hsa-mir-874 | 5/73 (7%) | 5q31.3; 3/50 (6%) | |
| 5q35.2 | loss | RP11-489P1 | RP11-31J6 | 2.22 | MSX2 | 5/73 (7%) | 5q34; 4/50 (8%) | |
| 5q35.3 | loss | RP11-365H22 | RP11-703G5 | 1.04 | ADAMTS6 | 5/73 (7%) | 5q34; 4/50 (8%) | |
| 6q15-16.1 | loss | RP1-23D17 | RP1-154G14 | 2.54 | CASP8AP2 | 9/73 (12%) | 6q16.2-3; 5/50 (10%) | 6q16.3-q21; 1/7 (14%) |
| 6q23.3 | gain | RP1-32B1 | RP11-323N12 | 0.24 | MYB, hsa-mir-548a-2 | 6/72 (8%) | 6q23.3; 5/50 (10%) | 6q23.3; 1/7 (14%) |
| 7p14.1 | loss | RP11-302L6 | RP11-273L18 | 0.91 | TCRG | 24/73 (33%) | NA | |
| 7q22.1 | gain | RP4-808A1 | RP11-757A13 | 0.86 | SMURF1,*TRRAP | 5/73 (7%) | ||
| 7q31.1 | gain | RP11-5N18 | RP11-238I13 | 1.12 | DNAJB9 | 4/73 (5%) | ||
| 9p21.3 | loss | RP11-149I2 | RP11-149I2 | 0.15 | CDKN2A, CDKN2B, MTAP | 45/72 (63%) | 9p21.3; 36/50 (72%) | 9p21.3; 5/7 (71%) |
| 9q31.1 | loss | RP11-515J13 | RP11-342F21 | 0.53 | Q5VW05 | 6/72 (8%) | ||
| 10q23.2-23.31 | loss | RP11-77F13 | RP11-765C10 | 0.48 | PTEN* | 4/72 (6%) | 10q23.31; 3/50 (6%) | |
| 11p15.5 | gain | RP11-295K3 | RP11-113A6 | 0.85 | IGF2,*hsa-mir-675, 483 | 4/72 (6%) | ||
| 11q13.1 | gain | RP11-141J21 | RP11-665N17 | 0.42 | MAP4K2, RASGRP2, hsa-mir-194-2, 192 | 4/72 (6%) | ||
| 11q14.2 | loss | RP11-90K17 | RP11-878E11 | 0.37 | PICALM | 4/71 (6%) | ||
| 12p13.2 | loss | RP11-180M15 | RP11-59H1 | 0.35 | CDKN1B,*hsa-mir-614, 613 | 8/69 (12%) | 12p13.2; 4/50 (8%) | |
| 13q33.3 | gain | RP11-153i24 | RP11-330C15 | 0.34 | TNFSF13B | 6/70 (9%) | ||
| 17p13.2 | loss | RP11-373N8 | RP11-803F22 | 0.39 | NALP1 | 4/73 (5%) | 17p13.3-11.2; 2/50 (4%) | |
| 17q23.2 | gain | RP11-19F16 | RP11-159D12 | 0.93 | MSI2,*VEZF1 | 4/73 (5%) | ||
| 17q23.3 | gain | RP11-156L14 | RP11-630H24 | 1.30 | SMURF2,*MAP3K3, hsa-mir-633 | 4/73 (5%) | ||
| 17q24.1-24.2 | gain | RP11-115N5 | RP11-4F22 | 0.67 | PRKCA* | 4/72 (6%) | ||
| 17q25.1 | gain | RP11-155C2 | RP11-478P5 | 0.53 | GPRC5C, GPR142 | 4/73 (5%) | ||
| 18q21.1 | loss | RP11-729G3 | RP11-1E21 | 0.71 | SMAD4* | 7/73 (10%) | ||
| 19p13.3 | gain | CTB-31O20 | RP11-660O21 | 2.00 | MKNK2* | 7/73 (10%) | ||
| 19p13.2 | gain | CTD-2560C1 | CTD-2102F19 | 0.77 | INSR | 4/73 (5%) | ||
| 19q13.33 | gain | CTC-273B12 | RP11-699H21 | 0.32 | RASIP1, FUT2 | 4/69 (6%) |
| Localization . | Type of aberration . | Start clone . | End clone . | Size, Mb . | Candidate gene(s)†/miRNA‡ . | Frequency . | Minimally overlapping region,§ n (%) . | Minimally overlapping region,‖ n (%) . |
|---|---|---|---|---|---|---|---|---|
| 3q12.1 | loss | RP11-121C1 | RP11-201E8 | 0.46 | COL8A1 | 5/73 (7%) | ||
| 3q13.11-13.12 | loss | RP11-16N5 | RP11-25F15 | 2.70 | CBLB,*ALCAM | 4/73 (5%) | ||
| 5q31.1-31.2 | loss | RP1-186K10 | CTB-46B19 | 1.52 | CTNNA1, hsa-mir-874 | 5/73 (7%) | 5q31.3; 3/50 (6%) | |
| 5q35.2 | loss | RP11-489P1 | RP11-31J6 | 2.22 | MSX2 | 5/73 (7%) | 5q34; 4/50 (8%) | |
| 5q35.3 | loss | RP11-365H22 | RP11-703G5 | 1.04 | ADAMTS6 | 5/73 (7%) | 5q34; 4/50 (8%) | |
| 6q15-16.1 | loss | RP1-23D17 | RP1-154G14 | 2.54 | CASP8AP2 | 9/73 (12%) | 6q16.2-3; 5/50 (10%) | 6q16.3-q21; 1/7 (14%) |
| 6q23.3 | gain | RP1-32B1 | RP11-323N12 | 0.24 | MYB, hsa-mir-548a-2 | 6/72 (8%) | 6q23.3; 5/50 (10%) | 6q23.3; 1/7 (14%) |
| 7p14.1 | loss | RP11-302L6 | RP11-273L18 | 0.91 | TCRG | 24/73 (33%) | NA | |
| 7q22.1 | gain | RP4-808A1 | RP11-757A13 | 0.86 | SMURF1,*TRRAP | 5/73 (7%) | ||
| 7q31.1 | gain | RP11-5N18 | RP11-238I13 | 1.12 | DNAJB9 | 4/73 (5%) | ||
| 9p21.3 | loss | RP11-149I2 | RP11-149I2 | 0.15 | CDKN2A, CDKN2B, MTAP | 45/72 (63%) | 9p21.3; 36/50 (72%) | 9p21.3; 5/7 (71%) |
| 9q31.1 | loss | RP11-515J13 | RP11-342F21 | 0.53 | Q5VW05 | 6/72 (8%) | ||
| 10q23.2-23.31 | loss | RP11-77F13 | RP11-765C10 | 0.48 | PTEN* | 4/72 (6%) | 10q23.31; 3/50 (6%) | |
| 11p15.5 | gain | RP11-295K3 | RP11-113A6 | 0.85 | IGF2,*hsa-mir-675, 483 | 4/72 (6%) | ||
| 11q13.1 | gain | RP11-141J21 | RP11-665N17 | 0.42 | MAP4K2, RASGRP2, hsa-mir-194-2, 192 | 4/72 (6%) | ||
| 11q14.2 | loss | RP11-90K17 | RP11-878E11 | 0.37 | PICALM | 4/71 (6%) | ||
| 12p13.2 | loss | RP11-180M15 | RP11-59H1 | 0.35 | CDKN1B,*hsa-mir-614, 613 | 8/69 (12%) | 12p13.2; 4/50 (8%) | |
| 13q33.3 | gain | RP11-153i24 | RP11-330C15 | 0.34 | TNFSF13B | 6/70 (9%) | ||
| 17p13.2 | loss | RP11-373N8 | RP11-803F22 | 0.39 | NALP1 | 4/73 (5%) | 17p13.3-11.2; 2/50 (4%) | |
| 17q23.2 | gain | RP11-19F16 | RP11-159D12 | 0.93 | MSI2,*VEZF1 | 4/73 (5%) | ||
| 17q23.3 | gain | RP11-156L14 | RP11-630H24 | 1.30 | SMURF2,*MAP3K3, hsa-mir-633 | 4/73 (5%) | ||
| 17q24.1-24.2 | gain | RP11-115N5 | RP11-4F22 | 0.67 | PRKCA* | 4/72 (6%) | ||
| 17q25.1 | gain | RP11-155C2 | RP11-478P5 | 0.53 | GPRC5C, GPR142 | 4/73 (5%) | ||
| 18q21.1 | loss | RP11-729G3 | RP11-1E21 | 0.71 | SMAD4* | 7/73 (10%) | ||
| 19p13.3 | gain | CTB-31O20 | RP11-660O21 | 2.00 | MKNK2* | 7/73 (10%) | ||
| 19p13.2 | gain | CTD-2560C1 | CTD-2102F19 | 0.77 | INSR | 4/73 (5%) | ||
| 19q13.33 | gain | CTC-273B12 | RP11-699H21 | 0.32 | RASIP1, FUT2 | 4/69 (6%) |
″Start clone″ and ″end clone″ designations reflect NCBI-recommended clone nomenclature and library nomenclature. Amp indicates amplifications; and del, deletions.
Candidate genes involved in TFG-β or PI3K-AKT signaling.
Candidate genes within the listed DNA copy-number aberrations were selected based on putative and reported cancer-related function.
Known miRNA genes within the reported DNA copy-number aberrations.
From Mullighan et al.43
From Kuiper et al.42