Fig. 2: Timing metastatic divergence.

a, Example phylogenetic trees depicting early (CRUK0587) and late (CRUK0236) divergence. Light purple, shared; dark purple, metastasis-unique; green, primary-unique mutation clusters. b, Pie chart showing the fraction of cases with early (n = 32) and late divergence (n = 94) (left panel). The proportion of early and late divergence by metastasis type at the sample level (primary LN/satellite versus recurrence/progression; Fisher’s exact test, P = 0.61)  (right panel). c, In early divergence cases, the median number of pre-WGD mutations (blue line) defined as not clonal in the metastases is 1.4% (IQR = 0.8–3.2%; n = 28). Post-WGD mutations or mutations in non-WGD tumours (red line) were more likely to be not clonal in the metastasis (median = 8.5%, IQR = 3.0–22.3%; n = 32; Wilcoxon rank-sum test, P = 0.003). d, Downsampling of late divergence cases (n = 94). A random set of primary tumour regions was used to re-classify the timing of divergence for each case (top panel); proportion of shared mutations between downsampled primary tumour and metastases (bottom panel). e, Phylogenetic trees for case CRUK0590 (inner circle) and within each region, depicting an active platinum signature in the occipital metastasis, timing metastatic divergence of the occipital and cerebellar metastases to a period when platinum therapy was delivered, approximately 6–8 months before recurrence. f, Simulations of tumour size (n = 20 simulations per tumour size) at metastatic clone divergence suggest that early divergence is more likely to happen when the primary tumour is small; a diameter ≥8 mm is a typical threshold used to investigate solid nodules detected using computed tomography^{10,11,12,13,14,15,16} (denoted ‘actionable’). The box plots represent the upper and lower quartiles (box limits), the median (centre line) and the vertical bars span the 5th to 95th percentiles. All tests were two-sided unless otherwise specified. R, region; LN, lymph node; WGD, whole genome doubling.