Extended Data Fig. 8: Oncogene frequency on ecDNA.
a, (top) Bar plot showing the frequency of amplifications of any kind (either ecDNA or chromosomal) affecting oncogenes in the GEL cohort. (middle) Box plots of copy number for oncogenes when affected by chromosomal amplifications (yellow) or ecDNA (red). (bottom) Stacked bar plot showing the proportion of amplifications for each oncogene that are chromosomal (yellow) or ecDNA (red). b, Heatmap showing oncogenes recurrently amplified (n > 18) on ecDNA by cancer type. Tissue type is indicated by the coloured bar at the top of the heatmap. The colour of each cell indicates the relative frequency of its occurrence compared to all other oncogenes on ecDNA. The total number of ecDNAs carrying a particular oncogene is displayed to the right of the heatmap before the name of the oncogene. Genes marked with an asterisk are those also present in the IntOGen database36 and the Cancer Gene Census. c, Scatter plots for each tissue type showing the dN/dS estimates of genes in the GEL cohort (x-axis) versus fraction of the genes subject to amplification (y-axis). Oncogenes are represented by red dots, tumour suppressor genes by yellow dots, and non-cancer genes by grey dots. “sig. amp” is an abbreviation for “significantly amplified” and “sig. dNdS” is an abbreviation for “significant by dNdSvc analysis”. Only genes significantly amplified and found significant by dN/dS analysis are annotated and are found in the top right quadrant of each subplot for a tissue type. Only tissue types with sufficient mutations and amplifications for the analysis were included.
