Table 2.
Frequency of amplifications and deletions in a focused analysis of 32 genomic regions which were either previously known to be of interest in urothelial cancer or which were identified by TCGA as having statistically significant focal copy number changes
| Pathway | Gene | % alterations in primaries (n = 29) | % alterations in metastasis (n = 30) |
|---|---|---|---|
| MAP kinase pathway | ERBB2^ | 2/29-7% | 4/30-13% |
| FGFR3^ | 0/29-0% | 1/30-3% | |
| FGFR1^ | 2/29-7% | 4/30-13% | |
| EGFR^ | 0/29-0% | 0/30-0% | |
| MET^ | 0/29-0% | 0/30-0% | |
| KRAS^ | 0/29-0% | 0/30-0% | |
| NF1^ | 0/29-0% | 1/30-3% | |
| BRAF^ | 0/29-0% | 0/30-0% | |
| RAF1^ | 1/29-3% | 3/30-10% | |
| MYC^ | 0/29-0% | 2/30-7% | |
| MYCL1^ | 5/29-17% | 3/30-10% | |
| P53 pathway | MDM2^ | 1/29-3% | 3/30-10% |
| TP53 ∨ | 2/29-7% | 2/30-7% | |
| RB pathway* | CDKN2A ∨ | 8/29-28% | 10/30-33% |
| CDK4 ^ | 1/29-3% | 2/30-7% | |
| CCND1 ^ | 2/29-7% | 6/30-20% | |
| CCNE1^ | 2/29-7% | 4/30-13% | |
| RB1 ∨ | 0/29-0% | 2/30-7% | |
| E2F3^ *(p = 0.04) | 2/29-7% | 9/30-30% | |
| PI3K pathway | PTEN ∨ | 1/29-3% | 1/30-3% |
| PIK3CA^ | 0/29-0% | 0/30-0% | |
| AKT1^ | 0/29-0% | 1/30-3% | |
| TSC1 ∨ | 1/29-3% | 1/30-3% | |
| MTOR^ | 0/29-0% | 0/30-0% | |
| Others | BCL2L1^ | 1/29-3% | 1/30-3% |
| PPARG^ | 1/29-3% | 5/30-17% | |
| CREBBP ∨ | 0/29-0% | 1/30-3% | |
| PVRL4^ | 2/29-7% | 7/30-23% | |
| YWHAZ^ | 5/29-17% | 4/30-13% | |
| NCOR1 ∨ | 2/29-7% | 1/30-3% | |
| YAP1^ | 0/29-0% | 1/30-3% | |
| ZNF703^ | 1/29-3% | 3/30-10% | |
| n = 928 | n = 960 | ||
| % total loci with amplification/deletion* | (p < 0.001) | 42/928-4.5% | 83/960-8.6% |
*p <0.05 Fishers exact test, ^=amplification, ∨ = deletion.
The data are represented using a threshold of log2 copy number ratio >0.8 for amplification and log2 copy number ratio < −0.8 for deletion. Data are shown in tabular format with frequency of amplifications and deletions of genes outlined. ^denotes amplifications and ˇdenotes deletions.