Extended Data Fig. 2: Genomic characteristics of RT-associated small deletions.

a, Comparison of mean deletion lengths of acquired deletions in RT- vs RT + IDHmut gliomas. Two-sided Mann-Whitney U test. b, Metastatic cohort: Boxplots depicting mean deletion lengths in RT-naïve (left) and palliative RT-treated (middle) and curative RT-treated (right) tumor samples separated by primary tumor location. Two-sided Kruskal-Wallis test. c, Longitudinal comparison (X-Axis) of mean distances of deletions to non-B DNA features in kb (Y-Axis) in IDHmut glioma cases. Cases separated by radiation treatment and hypermutation. Note that neither in hypermutated, nor in RT-naïve non-hypermutated glioma samples significant longitudinal differences were observed. Two-sided paired Wilcoxon signed-rank test. d, Gene-wise dN/dS estimates by RT (rows) and fraction (columns) in GLASS. Two-sided likelihood ratio tests. Genes sorted by Q-value (Bonferroni-adjusted P-value) and P-value. Q-values indicated in color, whereas P-values shown in light grey. Q-value threshold of 0.05 indicated by a horizontal red line. e, Comparison of proportion of deletions for IDHmut glioma samples separated by RT and hypermutation. Two-sided paired Wilcoxon signed-rank test. For each sample, the proportion of deletions with 1 bp length, > 1 bp length with microhomology and > 1 bp length without microhomology add up to 1. Bottom right panels (RT-received non-hypermutators) presented in Fig. 2d and shown here for comparison with other groups. f, Comparison of proportion of deletions in metastatic cohort between RT-treated and RT-naïve cases using two-sided Kruskal-Wallis test. In bone/soft tissue, breast and head & neck and nervous system cancers, significantly lower proportions of deletions >1 bp with microhomology were observed in RT-treated samples compared to RT-naïve samples. In contrast, RT-received breast, colon/rectum, esophagus, nervous system and prostate tumor samples showed significantly higher proportions in deletions > 1 bp without microhomology. Boxes span quartiles, center lines as medians, whiskers represent absolute range, excluding outliers.