Extended Data Fig. 9: Comparison of VAF at TCN and other contexts.

(a) C>G and C>T variants at TCN contexts have a similar median VAF to those at other contexts. Cases with tumor purity <50% and those with no attribution of APOBEC mutational signatures (COSMIC signatures SBS2 and SBS13) were excluded from the analysis (n=172 biologically independent samples). Box and whiskers plots are in the style of Tukey. The line within the box is plotted at the median while the upper and lower ends are indicated 25th and 75th percentiles. Whiskers show 1.5*IQR (interquartile range) and values outside it are shown as individual data points. (b) There is no shift in the median VAF (Median VAF(TCN) – Median VAF (other contexts)) of C>G and C>T variants at TCN contexts compared to variants at other contexts. Cases with tumor purity <50% and those with no attribution of APOBEC mutational signatures (COSMIC signatures SBS2 and SBS13) were excluded from the analysis. (c) No significant difference was found in the median VAF of C>G and C>T variants at TCN contexts compared to all other contexts in any individual country (n=170 biologically independent samples). UK cases were not included as only two cases were of sufficient purity. Countries are ordered by approximate incidence rate in ascending order. Box and whiskers plots are in the style of Tukey. The line within the box is plotted at the median while the upper and lower ends are indicated 25th and 75th percentiles. Whiskers show 1.5*IQR (interquartile range) and values outside it are shown as individual data points.