High-level DNA amplifications and homozygous deletions
| Chromosome amp/del . | n (%) . | Start clone . | End clone . | Size, Mb . | Genes amp/del . | Candidate genes†/miRNA‡ . | Minimally overlapping region§ n (%)¶ . | Minimally overlapping region,‖ n (%)¶ . |
|---|---|---|---|---|---|---|---|---|
| del 9p21.3 | 24 (33%) | RP11-149I2 | RP11-149I2 | 0.20 | 4 | CDKN2A, CDKN2B | del 9p21.3; 36/50 (72%) | del 9p21.3; 5/7 (71%) |
| del 10q23.31 | 1 (1%) | RP11-165M8 | RP11-765C10 | 0.36 | 4 | PTEN | del 10q23.31; 3/50 (6%) | |
| del Xq26.2 | 1 (1%) | RP11-689E9 | RP6-198C21 | 2.16 | 13 | TFDP3 | ||
| amp 6q23.3 | 1 (1%) | RP1-32B1 | RP11-323N12 | 0.24 | 2 | MYB, AHI1, hsa-mir-548a-2 | amp 6q23.3; 5/50 (10%) | amp 6q23.3; 1/7 (14%) |
| amp 9q34.13 | 1 (1%) | RP11-57C19 | RP11-143H20 | 0.55 | 11 | ABL1, NUP241 |
| Chromosome amp/del . | n (%) . | Start clone . | End clone . | Size, Mb . | Genes amp/del . | Candidate genes†/miRNA‡ . | Minimally overlapping region§ n (%)¶ . | Minimally overlapping region,‖ n (%)¶ . |
|---|---|---|---|---|---|---|---|---|
| del 9p21.3 | 24 (33%) | RP11-149I2 | RP11-149I2 | 0.20 | 4 | CDKN2A, CDKN2B | del 9p21.3; 36/50 (72%) | del 9p21.3; 5/7 (71%) |
| del 10q23.31 | 1 (1%) | RP11-165M8 | RP11-765C10 | 0.36 | 4 | PTEN | del 10q23.31; 3/50 (6%) | |
| del Xq26.2 | 1 (1%) | RP11-689E9 | RP6-198C21 | 2.16 | 13 | TFDP3 | ||
| amp 6q23.3 | 1 (1%) | RP1-32B1 | RP11-323N12 | 0.24 | 2 | MYB, AHI1, hsa-mir-548a-2 | amp 6q23.3; 5/50 (10%) | amp 6q23.3; 1/7 (14%) |
| amp 9q34.13 | 1 (1%) | RP11-57C19 | RP11-143H20 | 0.55 | 11 | ABL1, NUP241 |
“Start clone” and “end clone” designations reflect NCBI-recommended clone nomenclature and library nomenclature. Amp indicates amplifications; and del, deletions.
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
Authors did not distinguish between DNA copy-number gains and amplifications.