Table 2.
Prioritized list of genes showing the strongest evidence of involvement in defining chemoresponse to epirubicin/cyclophosphamide in breast cancer
| Gene | Selected against (A) or for (B)? | No of tumours? | Damaging predictions? | Pathway (yes/no)? | Priority total |
|---|---|---|---|---|---|
| TCHH | A | 3 | 3 | N | 6 |
| MUC17 | B | 2 | 3 | N | 5 |
| ARAP2 | A | 3 | 2 | N | 5 |
| FLG2 | B | 3 | 2 | N | 5 |
| ABL1 | A | 3 | 2 | N | 5 |
| CENPF | A | 2 | 3 | N | 5 |
| COL6A3 | A | 2 | 2 | Y; collagen proteins | 5 |
| DMBT1 | A | 4 | 1 | N | 5 |
| ITGA7 | A | 2 | 2 | Y; integrin signalling pathway | 5 |
| PLXNA1 | A | 2 | 3 | N | 5 |
| S100PBP | A | 2 | 3 | N | 5 |
| SYNE1 | A | 3 | 2 | N | 5 |
| ZFHX4 | A | 2 | 3 | N | 5 |
| CACNA1C | B | 2 | 2 | Y; type II diabetes mellitus | 5 |
Genes were identified that hosted somatic variants showing selection by therapy. Genes were prioritized on the basis of how many cases showed a consistent direction of selection (column 3), how many variants were predicted to be damaging (column 4), and whether the gene functions in a pathway that was over-represented in the lists of genes showing selection (column 5). These factors were combined (column 3 + column 4 + 1 if Y in column 5) to give a final prioritization score (column 6)