Extended Data Fig. 10: SCNAs in metastatic samples.

a, Beeswarm plot indicating the total proportion of the genome affected by either clonal or subclonal SCNAs in primary tumour samples (red dots) or metastatic samples (blue dots). The black bars indicate the median of the distribution. A two-sided unpaired Student’s t-test was used in this comparison; the P value and effect size(es) are shown. b, Difference in the percentage of the genome affected by SCNAs between paired metastatic and primary tumour samples (n = 152). The waterfall plot shows whether a greater or lesser proportion of the genome was affected by total SCNAs in the primary or metastatic sample(s) of tumours with at least one primary tumour sample and at least one metastatic sample. Purple bars indicate that a greater proportion of the genome was affected by total SCNAs in the metastatic sample and pink bars indicate a greater proportion was affected in the primary tumour sample. A two-sided paired Student’s t-test was used for this comparison. c, Beeswarm plots indicating, for each primary tumour and metastatic sample, the proportion of the genome impacted by SCNAs. These are the same samples included in the analysis of a. The black bars indicate the median of the distribution. Two-sided unpaired Student’s t-tests were used for each comparison; P values are indicated at the top of each plot. d, Beeswarm plots indicating for each primary tumour and metastatic sample the proportion of SCNAs that is subclonal. These are the same samples included in the analysis of a. The black bars show the median of the distribution. Two-sided unpaired Student’s t-tests were used for each comparison; P values are indicated at the top of each plot. e, Shared and private primary tumour and metastatic LOH. Bar plots separated by tumour type with each stacked bar representing the LOH identified in a single tumour sample with both primary tumour and metastatic samples. Each bar is coloured according to the proportion of LOH identified in that tumour that is shared between the primary tumour and metastatic samples (blue), the proportion of LOH present only in primary tumour samples (green) or the proportion of LOH present only in metastatic samples (red). The grey horizontal lines show the median value of the proportion of LOH shared between primary tumour and metastatic samples for each tumour type. f–i, Chromosomal arm-level events enriched in metastatic samples. We included only the four tumour types with >10 tumours with paired primary tumour–metastatic samples: LUAD (f), ER⁺ breast cancer (g), HER2⁺ breast cancer (h) and KIRC (i). In each panel, all chromosome arms are featured. The bar plots show the number of tumours with arm-level SCNAs in each tumour type. The colour of the bars indicates whether that arm-level event was enriched, depleted or maintained in the metastatic sample when compared with the corresponding primary tumour sample from the disease of the same patient. Bars facing right represent gain SCNAs; bars facing left represent loss SCNAs. The rectangular blocks between the bar plots indicate whether the arm-level events were recurrent events. Orange blocks represent recurrent subclonal events; grey blocks represent recurrent clonal events; blocks that are partially grey and partially orange represent events that are clonally and subclonally recurrent. The asterisks indicate whether the arm-level event is significantly enriched in metastatic samples in the combined paired (two-sided binomial test) and unpaired (test of equal or given proportions) primary tumour–metastatic analysis.