Table 2. Copy number of putative target genes in areas of chromothripsis amplification.
| Chr ▸ |
5 |
12 |
17 |
|||||
|---|---|---|---|---|---|---|---|---|
| Gene ▸ | TERT | RICTOR | CCND2 | MDM2 | CDK4 | TP53 | COPS3 | NF1 |
| Sample ▾ | ||||||||
| PD13486a | − | +3 | ||||||
| PD7190a | +1 | +6 | ||||||
| PD9962a | +5 | +2 | ||||||
| PD13490a | +4 | +7 | LOH | +13 | BP | |||
| PD13478a | +1 | +20 | +22 | |||||
| PD13495a | +1 | +5 | − | |||||
| PD7401a | +6 | +10 | +8 | |||||
| PD7508a | +2 | +17 | +23 | |||||
| PD13492a | +1 | − | +15 | LOH+BP | +16 | − | ||
| PD13476a | LOH+BP | +16 | LOH | |||||
| PD7513a | LOH+BP | +25 | LOH | |||||
| PD9056a | LOH+BP | +26 | − | |||||
BP, breakpoint present within gene footprint; Chr, chromosome; LOH, loss of heterozygosity.
Allele-specific copy number of putative target genes in regions with chromothripsis amplification. For oncogenes (TERT, RICTOR, CCND2, MDM2, CDK4, COPS3) copy number gain of the major allele is shown. For tumour suppressor genes (TP53, NF1) the minor allele is shown. Numbers preceded by ‘+’ indicate number of extra copies. The bold cells indicate significant copy number gain, the italicized cells indicate significant copy number loss.