Extended Data Fig. 4: The influence of time between the biopsies on the discordance of genome-wide somatic profiles between paired biopsies.

a, Dot plots of the ascsin-transformed fractions of genomic alterations private to the first biopsy (lost alterations, as a fraction of the total number of alterations in the first biopsy; top row of plots; y-axis), or the ascsin-transformed fraction of genomic alterations private to the second biopsy (gained alterations, as a fraction of the total number of alterations in the second biopsy; bottom row of plots; y-axis) for all biopsy pairs (n = 250), against the time between biopsies (x-axis). Different classes of somatic alterations are plotted separately: nucleotide substitutions (clonal, subclonal), indels (clonal, subclonal), and structural variants (SVs), as indicated at each subplot’s title. Clonal alterations have a probability of clonality above >95%, whereas subclonal alterations have a probability of subclonality >95%. Arcsin transformation was performed to achieve normality of the inherently non-normally distributed fractions. Linear fits and bootstrapping-obtained 95% confidence intervals are plotted. Pearson correlation coefficients (r) and accompanying two-sided P-values are shown (red for significant associations). b, As A, but the y-axis indicates the Pearson correlation coefficient (r) for the copy number profiles of biopsy pairs. Analysis is based on all paired biopsies (n = 250).