Fig. 3: Delineation of metastatic evolution before chemotherapy.

All six patients were treated with cisplatin-based chemotherapy upon detection of metastatic disease. a Location of metastasis and the time to recurrence (mo = months). P = primary tumor, M = metastasis. The images were created using Biorender.com. b Clonal relationships between primary tumor samples and metastatic lesions depicted by phylogenetic trees. Trunk/branch lengths correspond to the number of SNVs. Mutations in genes involved in DDR, frequently mutated in TCGA or identified as drivers in BC (IntOGen⁶²) are indicated. Green = trunk, yellow = branch, blue = primary tumors, pink = metastatic lesions. c Variant allele frequencies for mutations identified in either of the available samples per patient. Identified mutations were subjected to read-counting in processed bam files to enable identification of mutations called in one sample, and present, but not called in another sample. The required read depth for identifying a given mutation was calculated for every position based on the lowest observed allele frequency. Only positions with sufficient read depth in all investigated samples were included. d Box plots depicting the observed allele frequencies for trunk and branch mutations. Asterisks indicate p-values below 2.2e−16. e Relative contribution of mutational signatures in the trunks (left circles) and branches (right circles). P-values were calculated using a Wilcoxon rank-sum test. For all boxplots, the center line represents the median, box hinges represent first and third quartiles, whiskers represent ±1.5 × interquartile range (IQR) and points represent outliers. Source data are provided as a Source data file.