Table 1.
Known cancer-relevant mutations (in tumor-suppressor genes and proto-oncogenes) detected in the tumor samples harvested prechemotherapy (T1) and postchemotherapy (T2)
| Gene | HGVS protein | Genomic change | AF pre | AF post | Variant consequence | Predicted effect | dbSNP ID |
|---|---|---|---|---|---|---|---|
| LATS2 | p.Val901SerfsTer43 | 13:g.21553902T>TC | 0.55 | 0.53 | Frame shift | - | - |
| LATS1 | p.Trp879Ter | 6:g.149997831C>T | 0.66 | 0.55 | Stop gained | Damaging | - |
| MECOM | p.Pro88Ser | 3:g.169099088G>A | 0.34 | 0.19 | Missense | Damaging | - |
| OPCML | p.Gln49Glu | 11:g.132812843G>C | 0.04 | - | Missense | Tolerated | - |
| GATA3a | p.Pro189Leu | 10:g.8100592C>T | - | 0.13 | Missense | Mixed | - |
| EPHA3 | p.Gly114Ter | 3:g.89259196G>T | - | 0.15 | Stop gained | Damaging | - |
| GLI1 | p.Cys177Trp | 12:g.57859035C>G | - | 0.04 | Missense | Damaging | - |
| CABLES1 | p.Gln631His | 18:g.20837322G>C | - | 0.03 | Missense | Tolerated | - |
| CASC1 | p.Gly242Ter | 12:g.25297577C>A | - | 0.05 | Stop gained | Tolerated | - |
| ANAPC1 | p.Gln451His | 2:g.112615888C>G | - | 0.04 | Missense | Tolerated | 79100806 |
The predicted effect represents the majority prediction of several algorithms included in dbNSFP v3.5. AF, allelic fraction.
aAlthough not considered a proto-oncogene or tumor suppressor per se, we also include the transcription factor GATA3 because of its reported association to breast cancer.