Fig. 3: Genetic variants identified at the DNA and RNA level in tumor tissue from different cancer entities.

a Distribution of the total numbers of variants identified from DNA (upper panel) and RNA data (lower panel) identified per tumor sample grouped by tumor entity. Mutations were called by MuTect2 (v4.1.0.0) from whole exome (WES)/whole-genome sequencing (WGS) data and by Strelka2 (v2.9.10) from RNA sequencing (RNA-seq) data. SNP-filtering was performed using the dbSNP-all database. No RNA data were available for patients IN-11-T1, IN-14, IN-16, IN-20, IN-25, IN-31, and IN-34. b Pie chart depicting the proportion of variants only identified from RNA-seq data of all tumor samples combined where the respective canonical sequence was identified at the DNA level with coverage of ≥3 reads (green) or the respective region was not covered at the DNA level (gray, <3 reads). c Distribution of the nucleotide exchange pattern overall single nucleotide variants only identified from RNA-seq data of all tumor samples combined. d Pie charts depicting the distribution of each mutation type for variants called from all DNA (left) and RNA (right) variants. e, f Pie charts showing the proportions of unique and shared DNA variants (e) and RNA variants (f) between different patients. The right bar graph shows the number of variants shared by 4 to 14 patients for DNA variants (e) and shared by 10 to 26 patients for RNA variants (f) in more detail. a–f n = 39 tumor samples from n = 32 patients for WES/WGS data; n = 32 tumor samples from n = 26 patients for RNA-seq data (see Supplementary Table 1). T tumor. Source data are provided as a Source Data file.