Extended Data Fig. 4: WGD across tumour types.

a, Bar plots indicating the number and proportion of tumours of each tumour type that show WGD. Subclonal WGD tumours are indicated in blue. b, Beeswarm plots comparing the proportion of the genome affected by clonal or subclonal SCNAs and mirrored subclonal allelic imbalance (MSAI) in WGD and non-WGD tumours. Black bars indicate the median of each distribution. Two-sided Student’s t-tests were used for each comparison. c, Comparing the proportion of the genome affected by clonal or subclonal SCNAs in matched WGD and non-WGD samples from tumours with subclonal WGD. Bars indicate, for each patient with subclonal WGD, the difference between the median proportion of the genome affected by SCNAs in WGD and non-WGD samples. The inset beeswarm plots compare the proportion  of the genome affected by different types of SCNAs in WGD and non-WGD samples. The black bars in the beeswarm plots represent the medians of each group. d–f, Impact of OG-TSG score on average arm-level copy number changes. Scatter plots showing the average subclonal arm-level change from MRCA in non-WGD (d; n = 171), WGD (e; n = 194) and subclonal WGD (f; n = 29) tumours versus arm OG–TSG score. Shaded areas indicate the 95% confidence interval. ρ and P values are from Spearman correlation tests. g, Scatter plot showing the average clonal (MRCA) copy number in the entire cohort (n = 394) versus chromosome arm size. h–j, Scatter plots showing the average subclonal arm-level change from MRCA in non-WGD (h; n = 171), WGD (i; n = 194) and subclonal WGD (j; n = 29) tumours versus chromosome size. Shaded areas indicate the 95% confidence interval. ρ and P values are from Spearman correlation tests.