Fig. 2

Changes in gene mutation, mutation burden, and the MSigDB pathway between the paired pre- and post-treatment tumor samples. Comparison of tumor purity (A) and mutation burden (B) between the 44 paired pre- and post-treatment tumors. P values are calculated based on the Wilcoxon signed-rank test. C The most frequently mutated genes before and after NAC. D Mutations associated with the MSigDB pathway in the pre- and post-treatment tumors. Bars on the top indicate the number of pathways affected in a given patient, and colored bars indicate if the variant was only found in the pre- or post-treatment tumors, or shared in both. P values in panels C and D are calculated based on the Pearson’s chi-square test; **P < 0.01, *P < 0.05