Fig. 1

Overall chemotherapy associated changes in genomic alterations. a Schematic overview of tumor tissue collection in the context of neoadjuvant cisplatin-based chemotherapy, followed by whole-exome sequencing and analysis. The 25th to 75th percentile time between diagnosis and cystectomy samples was 3.6–5.8 months. b Inferred changes in mutational load per patient from pre-treatment to post-treatment. Overall, there is no statistically significant change in the total mutational load (mean change = −17.3, paired t-test p = 0.20). c Breakdown of mutations private to the pre-treatment tumor, post-treatment tumor, and common to both. The mean number of “pre-only” mutations (private to pre-treatment tumor) and “post-only” mutations (private to post-treatment tumor) mutations is 64.7 (SD = 81.1) and 47.5 (SD = 46.9), respectively. d Boxplot of pre-treatment, shared, and post-treatment subclonal mutations. There are almost no shared subclonal mutations (median 3.5 mutations, 25th–75th percentile 1–15 mutations). There is a statistically significant difference between the number of inferred subclonal pre-treatment and shared, and shared and post-treatment mutations (Mann–Whitney U p = 1.2e-04, p = 1.9e-05 respectively). e Boxplot of pre-treatment, shared, and post-treatment clonal mutations. There is no statistically significant difference between the number of inferred clonal mutations in the pre-treatment tumors and shared between pre and post-treatment tumors, and shared mutations and post-treatment mutations (Mann–Whitney U p = 0.38, p = 0.51). SD Standard Deviation, N.S. Not statistically significant; “*”Indicates p < 0.05; “**”Indicates p < 0.01