Table 2.
Characteristics of the 22 patients with pre-and post chemotherapy matched samples.
| StudyID | Histology | Regimen | NRI | RCB | Grade | T-stage | N-stage | Subtype | Recurrence | Recurrence location | Vital status | Exome seq | RNA seq | DNA_pre_TP | DNA_post_TP | RNA_pre_TP | RNA_post_TP |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 97 | IDC | 6× ddAC | 0.33 | 2 | NA | 2 | − | LUM | 0 | A | 1 | 1 | 70 | 80 | 70 | 75 | |
| 188 | IDC | 1×AC, 1×CD | 0 | 2 | 3 | 2 | − | TN | 1 | Lung, brain | D | 1 | 0 | 80 | 80 | ||
| 2046 | IDC | 6× ddAC | 0 | 3 | 3 | 2 | + | TN | 1 | Liver | D | 1 | 1 | 70 | 70 | 50 | 70 |
| 2271 | IDC | 6× ddAC | 0.33 | 2 | 3 | 2 | + | TN | 1 | Thorax, lymph, contralateral mamma, skin | D | 1 | 1 | 80 | 55 | 90 | 55 |
| 2472 | IDC | 4× ddAC, 2× CTC + PSCT | 0.33 | 3 | 2 | 2 | + | TN | 1 | Multiple lymph nodes, lung, liver | D | 0 | 1 | 80 | 70 | ||
| 2492 | IDC | 6× ddAC | 0.33 | 3 | 2 | 2 | + | TN | 1 | Brain | D | 1 | 1 | 90 | 50 | 60 | 50 |
| 2653 | IDC | 3× ddAC, 2× CD, 2× D | 0 | 2 | 2 | 2 | + | LUM | 1 | Bone | A | 0 | 1 | 60 | 50 | ||
| 2661 | Papillary carcinoma | 6× ddAC | 0.2 | NA | 1 | 4 | − | LUM | 0 | A | 1 | 1 | 90 | 80 | 90 | 80 | |
| 2677 | ILC | 6× ddAC | 0 | NA | 2 | 2 | − | LUM | 0 | A | 1 | 1 | 50 | 70 | 50 | 70 | |
| 2691 | IDC | 6× ddAC | 0.33 | 3 | 2 | 2 | + | LUM | 0 | A | 1 | 1 | 40a | 60 | 40a | 60 | |
| 2739 | IDC | 3× AC, 3× CD | 0.33 | 2 | 2 | 2 | + | LUM | 0 | A | 1 | 1 | 80 | 60 | 80 | 60 | |
| 2789 | IDC | 6× ddAC | 0.33 | 2 | 2 | 2 | − | LUM | 0 | A | 1 | 1 | 60 | 40 | 60 | 40 | |
| 2817 | IDC | 3× AC, 3× CD | 0 | 3 | 2 | 2 | + | LUM | 0 | A | 1 | 1 | 70 | 80 | 70 | 80 | |
| 2852 | IDC | 3× ddAC | 0 | 3 | 2 | 2 | + | LUM | 1 | Bone, liver | A | 1 | 1 | 70 | 60 | 70 | 60 |
| 2976 | IDC | 3× ddAC, 4× paclitaxel | 0 | 2 | 2 | 2 | − | LUM | 0 | A | 1 | 1 | 70 | 50 | 70 | 50 | |
| 3001 | IDC | 6× ddAC | 0 | 3 | 2 | 2 | + | LUM | 0 | A | 1 | 1 | 60 | 65 | 60 | 65 | |
| 3036 | IDC | 6× ddAC | 0.25 | 2 | 1 | 3 | + | LUM | 0 | A | 1 | 1 | 50 | 50 | 50 | 50 | |
| 3065 | IDC | 6x ddAC | 0 | 2 | 2 | 2 | + | LUM | 0 | A | 1 | 1 | 70 | 60 | 70 | 60 | |
| 3067 | ILC | 6x ddAC | 0 | 3 | 2 | 1 | + | LUM | 0 | A | 1 | 1 | 60 | 60 | 60 | 60 | |
| 3130 | IDC | 6x ddAC | 0 | 3 | 2 | 1 | + | LUM | 0 | A | 1 | 1 | 60 | 55 | 60 | 55 | |
| 3161 | IDC | 3x ddAC, 9× paclitaxel | 0 | 3 | 2 | 2 | + | LUM | 0 | A | 1 | 1 | 60 | 80 | 60 | 80 | |
| 3280 | Metaplastic | 3× ddAC, 3× carbo/paclitaxel | NA | NA | 3 | 2 | + | TN | 0 | A | 1 | 0 | 60 | 60 |
NRI Neoadjuvant Response Index, RCB residual breast cancer burden, IDC invasive ductal carcinoma, ILC invasive lobular carcinoma, ddAC dose-dense adriamycin + cyclophosphamide, CD capecitabine + docetaxel, CTC + PSCT cyclofosfamide-thiotepa-carboplatine and peripheral stem cell transplant, TN triple negative, LUM luminal, A alive, D dead, DNA_pre_TP tissue tumor percentage pre-treatment for DNA isolation, DNA_post_TP tissue tumor percentage post-treatment for DNA isolation, RNA_pre_TP tissue tumor percentage pre-treatment for RNA isolation, RNA_post_TP tissue tumor percentage post-treatment for RNA isolation.
aAlthough we applied a 50% cut-off for tumor percentage, one exception was taken along.