Figure 1

Mutation spectra of AA-bladder cancers and AA-UTUCs. (A,B) Somatic mutation proportions in trinucleotide contexts for bladder cancers (130T and 136T) from Taiwan with known AA exposure (A) and AA-UTUCs (9T and 20T) (B). The height of each bar (the y axis) represents the proportion of somatic mutations that fall into a particular trinucleotide mutational class, adjusted for the frequency of the trinucleotide in the exome (Table S3 in Additional file 1). Along the x axis the mutations are organized first by the nucleotide mutation itself: C > A (turquoise bars), C > G (orange bars), C > T (blue bars), A:T > T:A (red bars), T > C (green bars), T > G (brown bars). For each mutation, the 16 trinucleotide contexts are ordered by the flanking 5′ then 3′ nucleotides. Numbers in parentheses indicate counts of mutations for each single nucleotide substitution (for example, C > A, C > G). Cosine similarities for A:T > T:A mutations were as follows: between 9T and 20T (two UTUCs), 0.989; between 20T and 130T (a UTUC and a bladder cancer), 0.992; between 20T and 136T (a UTUC and a bladder cancer), 0.982. (C,D) Strand bias showing counts of A > T mutations (y axis) on the transcribed (T) and non-transcribed (N) strands. Many fewer somatic A > T mutations were observed on the transcribed than on the non-transcribed strand in both AA-bladder cancers and AA-UTUCs. P-values were computed by one-sided binomial tests compared with the null hypotheses of equal proportions of mutations on the transcribed and non-transcribed strands.