Table 1. Samples whole-genome sequenced in this study and a description of key clinical and biomarker parameters.
| Case | Age |
Intrinsic subtype |
Proportion cells Ki67 positive |
Ki67 response |
ER allred |
Clonal instability index | |||
|---|---|---|---|---|---|---|---|---|---|
| BL | SURG | BL | SURG | BL | SURG | ||||
| BRC10 | 57 | LumB | LumA | 0.492 | 0.035 | Sensitive | 6 | 4 | 0.246 |
| BRC11 | 84 | LumB | LumB | 0.25 | 0.417 | Resistant | 7 | 6 | 0.097 |
| BRC14 | 86 | LumB | LumA | 0.442 | 0.012 | Sensitive | 7 | 4 | 0 |
| BRC15 | 83 | LumB | LumA | 0.238 | 0.01 | Sensitive | 7 | 7 | 0.579 |
| BRC17 | 63 | LumB | LumA | 0.32 | 0.019 | Sensitive | 7 | 8 | — |
| BRC18 | 85 | LumB | LumA | 0.125 | 0 | Sensitive | 8 | 7 | — |
| BRC20 | 61 | LumB | LumB | 0.456 | 0.349 | Resistant | 4 | 6 | 0.856 |
| BRC21 | 73 | LumA | Normal | 0.058 | 0.019 | Sensitive | 7 | 6 | 1 |
| BRC22 | 64 | LumA | LumA | 0.008 | 0 | Sensitive | 6 | 7 | 0.533 |
| BRC24 | 51 | LumB | LumB | 0.152 | 0.155 | Resistant | 7 | 7 | 0.403 |
| BRC26 | 71 | LumB | LumA | 0.101 | 0.07 | Sensitive | 7 | 5 | 0.499 |
| BRC30 | 60 | LumB | LumA | 0.256 | 0.183 | Resistant | 5 | 5 | 0.371 |
| BRC32 | 54 | LumA | LumA | 0.1 | 0 | Sensitive | 7 | 6 | 0.450 |
| BRC37 | 56 | LumB | LumB | 0.76 | 0.308 | Resistant | 6 | 4 | 0.359 |
| BRC38 | 78 | LumB | Her2 | 0.162 | 0.471 | Resistant | 8 | 2 | 1 |
| BRC39 | 79 | LumB | LumA | 0.356 | 0.124 | Resistant | 6 | 5 | 0.841 |
| BRC40 | 66 | LumA | LumA | 0.076 | 0.008 | Sensitive | 8 | 8 | 0.904 |
| BRC41 | 55 | LumB | LumA | 0.412 | 0.008 | Sensitive | 8 | 6 | 0.535 |
| BRC42 | 74 | LumB | LumA | 0.081 | 0.022 | Sensitive | — | 8 | 0.341 |
| BRC48 | 66 | LumA | LumA | ND | 0.346 | Resistant | 6 | 6 | — |
| BRC49 | 56 | LumA | LumA | 0.077 | 0.152 | Resistant | 8 | 8 | 0.715 |
| BRC50 | 78 | LumA | LumA | 0.195 | 0.104 | Resistant | 4 | 5 | 0.856 |
ND, not determined. The clonal instability index is a metric of the amount of evolutionary change observed in the tumour, where higher numbers represent larger shifts and an index of 1 indicates completely unrelated tumours were present. A value of 0 indicates a monoclonal tumour with no post-treatment shift in clonality. Methodology to calculate the clonal instability index is defined in detail in the ‘Methods' section. BL refers to baseline and SURG the pathology specimen from the surgical resection after 16 to 18 weeks of AI therapy.