RUNX3 and intrahepatic cholangiocarcinoma: Compared to M class ICCs (92–147 somatic mutations; n = 5) with a relative deficit of CNAs, C class ICCs (54–84 mutations; n = 5) harbor recurrent focal CNAs including deletions involving CDKN2A, ROBO1, ROBO2, RUNX3, and SMAD4. We also show that transcriptome sequencing can be used for expression-based ICC categorization but the somatic mutation calling from the transcriptome can be heavily influenced by the gene expression level and potentially, by posttranscriptional modification such as nonsense mediated decay.