Table 4.
Molecular Profile Before and After Immunotherapy in a Breast Cancer Patient with 9p24.1 Amplification Using MSK-IMPACT
| Shared alteration | Before pembrolizumab | After pembrolizumab |
|---|---|---|
| Site | Metastasis, axillary lymph node | Sub-pectoral, chest wall mass |
| Tumor purity, morphology | 60% | 50% |
| Coverage | 1086× | 961× |
| Total number of shared mutations | 12 | 12 |
| ATM p.D1758N, c.5272 G>A | 23% | 19% |
| CDKN2Ap16INK4A p.R138T, c.413 G>C | 21% | 20% |
| ERCC5 p.E713K, c.2137 G>A | 29% | 19% |
| HLA-A p.V189M, c.565 G>A | 31% | 20% |
| MGA p.S300,* c.899C>G | 23% | 22% |
| MSH6 p.W50C, c.150 G>C | 19% | 19% |
| NOTCH4 p.E1836Q, c.5506 G>C | 16% | 18% |
| PIK3CA p.H1047R, c.3140A>G | 48% | 48% |
| RUNX1 p.D123fs, c.367dupG | 23% | 20% |
| SPEN p.E2260,* c.6778 G>T | 27% | 21% |
| SPEN p.E3305Q, c.9913 G>C | 24% | 19% |
| TP53 p.N29fs, c.86dupA | 42% | 37% |
| CNA, TCEB1, 8q21.1 | FC: 4.2 | FC: 4.4 |
| CNA, RAD21, 8q24.1 | FC: 3.3 | FC: 3.6 |
| CNA, MYC, 8q24.21 | FC: 3.3 | FC: 3.6 |
| CNA, NFKBIA, 14q13.2 | FC: 2 | FC: 3.1 |
Variant allele frequencies for alterations listed in column 1 are shown in columns 2 and 3.
CNA, copy number alteration; FC, fold change.