Fig. 3

Dynamics of copy number alterations during treatment. a, b Changes in copy number alterations (CNA) during sequential epirubicin and docetaxel treatment* a pre- to post-epirubicin and b pre- to post-docetaxel. Bars indicate the differences in fraction of patients with CNA (i.e., the difference: fraction of patients with CNAs in post-treatment samples minus the corresponding number in pretreatment samples). The Y-axis indicates the difference in copy number losses (blue) and gains (red). Chromosome numbers are indicated on the X-axis. Chromosomes and chromosome arms are separated by vertical lines and shaded background. For specific CNAs called as driver events in biopsies pretreatment, after epirubicin, and/or after docetaxel in individual patients, see Additional file 3: Fig. S10. c Parallel coordinate plots showing total copy number changes for MYC across the three time points (pretreatment, post-epirubicin, and post-docetaxel*), n = 51 tumors analyzed by whole exome sequencing (WES). The Y-axis indicates copy numbers, and the X-axis indicates the time points. Lines are colored based on the response to each of the two treatments. Asterisk: hormone receptor positive, HER2 normal (HR+HER2−) tumors; triangle: HER2+ tumors; squares: triple-negative breast cancers (TNBC). MYC copy numbers were significantly lowered during docetaxel treatment. d Parallel coordinate plots showing total copy number changes for ERRB2 across the three time points (pretreatment, post-epirubicin, and post-docetaxel/trastuzumab), n = 15 tumors/patients analyzed by WES. The Y-axis indicates copy numbers and the X-axis the time points. Lines are colored based on the response to each of the two treatments. Asterisk: HR+HER2− tumors, triangle: HER2+ tumors, squares: TNBC. ERBB2 copy numbers are significantly lower after docetaxel and trastuzumab treatment as compared to post-epirubicin tumors. *HER2-positive breast cancers received concomitant docetaxel and trastuzumab