Figure 1: Mutation spectrum revealed by whole-exome sequencing in 102 ICC patients.

(a) Somatic mutation density (mutations per Mb) in 102 ICC patients. Non-synonymous and synonymous are separated into two categories. (b) Proportion of six types of single-nucleotide substitutions in 102 patients sorted by the order as Fig. 1a. Different types of single nucleotide variants (SNVs) are consistently coloured in this figure. (c) Rate of different types of somatic mutations. (d) Mean of six types of SNVs and indels in 102 ICC patients. (e) Types of SNVs on transcribed strand and non-transcribed strand. P-value is estimated by paired Student’s t-test. (f) Triple-nucleotide mutation context. Six types of point mutations are reflected by six colour-coded blocks. Each block has 16 columns, indicating different flanking nucleotides of mutation sites. The ‘Pie chart’ shows the proportion of each type of point mutations. (g) Mutation signatures. The upper panel shows two mutation signatures predicted by the programme EMu. The lower panel shows the percentage of the contributions of two pathological features in each ICC patient, correlating with liver inflammation or fibrosis (upper), cirrhosis (middle) and liver inflammation, fibrosis or cirrhosis (lower).