Recurrent CNAs in 300 newly diagnosed adult and pediatric CBF-AMLs
| Lesion type and cytoband . | Loc. start† . | Loc. end† . | MDR size, Kb . | No. total lesions at locus . | No. t(8;21) lesions at locus . | No. inv(16) lesions at locus . | Gene and miRNA symbols (if < 15 or number) . |
|---|---|---|---|---|---|---|---|
| del(7q36.1)* | 151 119 304 | 151 766 515 | 647 | 23 | 10 | 13 | PRKAG2, GALNTL5, GALNT11, MLL3 |
| del(7q36.1)* | 148 970 700 | 150 326 128 | 1355 | 23 | 9 | 14 | 22 genes |
| del(7q33-34)* | 136 930 471 | 139 330 291 | 2400 | 19 | 7 | 12 | 18 genes |
| gain(8q24.21) | 130 655 287 | 130 793 607 | 138 | 30 | 16 | 14 | CCDC26 |
| del(9q21.32) | 84 807 339 | 85 927 065 | 1128 | 17 | 17 | 0 | RASEF, FRMD3, C9orf103, UBQLN1, KIF27, C9orf64, HNRNPK, RMI1;hsa-mir-7-1 |
| del(10q24.32-q24.33) | 104 388 971 | 104 991 787 | 602 | 2 | 1 | 1 | TRIM8, ARL3, SFXN2, C10orf26, CYP17A1, C10orf32, AS3MT, CNNM2, NT5C2 |
| del(11p13) | 32 406 375 | 32 535 970 | 130 | 7 | 2 | 5 | WT1, WIT1 |
| gain(11q25) | 133 855 317 | 134 223 724 | 368 | 5 | 0 | 5 | LOC238177 |
| gain(13q14.1-q23.2) | 82 686 052 | 114 126 487 | 31 440 | 5 | 0 | 5 | 473 genes; 9 miRNA |
| del(16p11.2) | 29 748 299 | 30 390 041 | 642 | 3 | 0 | 3 | 33 genes |
| del(17q11.2) | 26 543 169 | 27 444 641 | 901 | 6 | 0 | 6 | NF1, OMG, EVI2B, EVI2A, RAB11FIP4, C17orf79, UTP6, SUZ12, LRRC37B, SH3GLIP1;hsa-mir-193a, hsa-mir-365-2 |
| gain(22q11.21-q13.33) | 17 410 722 | 49 581 309 | 32 171 | 20 | 0 | 20 | 795 genes; 15 miRNA |
| -X | Whole chromosome | 11 | 11 | 0 | |||
| -Y | Whole chromosome | 44 | 42 | 2 | |||
| t(8;21) and inv(16) breakpoint-associated losses | |||||||
| del(8q21.3) | 93 152,074 | 93 180 996 | 29 | 13 | 13 | 0 | RUNX1T1 |
| del(21q22.12) | 35 124,310 | 35 130 211 | 6 | 16 | 16 | 0 | RUNX1 |
| del(16p13.11) | 15 725,642 | 15 738 236 | 13 | 28 | 0 | 28 | NDE1,MYH11 |
| del(16q22.1) | 65 676,333 | 65 712 933 | 36 | 21 | 0 | 21 | CBFB, C16orf70 |
| Lesion type and cytoband . | Loc. start† . | Loc. end† . | MDR size, Kb . | No. total lesions at locus . | No. t(8;21) lesions at locus . | No. inv(16) lesions at locus . | Gene and miRNA symbols (if < 15 or number) . |
|---|---|---|---|---|---|---|---|
| del(7q36.1)* | 151 119 304 | 151 766 515 | 647 | 23 | 10 | 13 | PRKAG2, GALNTL5, GALNT11, MLL3 |
| del(7q36.1)* | 148 970 700 | 150 326 128 | 1355 | 23 | 9 | 14 | 22 genes |
| del(7q33-34)* | 136 930 471 | 139 330 291 | 2400 | 19 | 7 | 12 | 18 genes |
| gain(8q24.21) | 130 655 287 | 130 793 607 | 138 | 30 | 16 | 14 | CCDC26 |
| del(9q21.32) | 84 807 339 | 85 927 065 | 1128 | 17 | 17 | 0 | RASEF, FRMD3, C9orf103, UBQLN1, KIF27, C9orf64, HNRNPK, RMI1;hsa-mir-7-1 |
| del(10q24.32-q24.33) | 104 388 971 | 104 991 787 | 602 | 2 | 1 | 1 | TRIM8, ARL3, SFXN2, C10orf26, CYP17A1, C10orf32, AS3MT, CNNM2, NT5C2 |
| del(11p13) | 32 406 375 | 32 535 970 | 130 | 7 | 2 | 5 | WT1, WIT1 |
| gain(11q25) | 133 855 317 | 134 223 724 | 368 | 5 | 0 | 5 | LOC238177 |
| gain(13q14.1-q23.2) | 82 686 052 | 114 126 487 | 31 440 | 5 | 0 | 5 | 473 genes; 9 miRNA |
| del(16p11.2) | 29 748 299 | 30 390 041 | 642 | 3 | 0 | 3 | 33 genes |
| del(17q11.2) | 26 543 169 | 27 444 641 | 901 | 6 | 0 | 6 | NF1, OMG, EVI2B, EVI2A, RAB11FIP4, C17orf79, UTP6, SUZ12, LRRC37B, SH3GLIP1;hsa-mir-193a, hsa-mir-365-2 |
| gain(22q11.21-q13.33) | 17 410 722 | 49 581 309 | 32 171 | 20 | 0 | 20 | 795 genes; 15 miRNA |
| -X | Whole chromosome | 11 | 11 | 0 | |||
| -Y | Whole chromosome | 44 | 42 | 2 | |||
| t(8;21) and inv(16) breakpoint-associated losses | |||||||
| del(8q21.3) | 93 152,074 | 93 180 996 | 29 | 13 | 13 | 0 | RUNX1T1 |
| del(21q22.12) | 35 124,310 | 35 130 211 | 6 | 16 | 16 | 0 | RUNX1 |
| del(16p13.11) | 15 725,642 | 15 738 236 | 13 | 28 | 0 | 28 | NDE1,MYH11 |
| del(16q22.1) | 65 676,333 | 65 712 933 | 36 | 21 | 0 | 21 | CBFB, C16orf70 |
CBF-AML indicates core-binding factor acute myeloid leukemia; CNA, copy number alterations; Loc., location on chromosome; and MDR, minimally detected regions.
In total, 25 cases with del(7q) were identified, with large overlapping deletions in most of the cases. Three distinct critical regions were defined by cases with focal deletions.
hg18.