Fig. 3. Genomic characteristics and clonal evolution following neoadjuvant treatment.

a Mutational landscape of pre-/post-treatment samples in 19 patients. The values of TMB, TNB, MSI scores, and tumor purity are shown in the upper panel. b Differences in TMB and TNB between MPR (n = 5) and non-MPR patients (n = 14). c Differences in TMB and TNB between MPR (n = 2) and non-MPR (n = 14) patients when MSI-H patients were excluded. Centers, boxes, and whiskers indicate medians, quantiles, and minima/maxima, respectively, in b and c, and two-sided Wilcoxon rank-sum test was used for comparison. d-e TMB changes in all paired specimens (n = 15), MSI-H-excluded patients (n = 14), and non-MPR patients (n = 13) before (d) and after (e) purity adjustment. Two-sided Wilcoxon signed-rank test was used for comparison in d and e. f Overall survival curves with and without SSPO mutation in TCGA STAD (n = 433) and Pan-Cancer (n = 9034) cohorts. Log-rank test was used for curve comparison. g Frequencies of mutation types that are classified according to VAF changes. “Lost” and “Gain” indicate unique mutations in pre- and post-therapy samples, respectively. “Increase” and “Decrease” indicate mutations whose VAF increased and decreased in post-therapy samples, respectively. h Correlation between “Lost” variants ratios and percentage of pathological regression across different patients, accessed by Spearman’s rank correlation coefficient (rho). The regression line is blue, and the shading indicates the 95% confidence interval. i Changes in cellular prevalence of tumor subclones. Error bars indicate standard deviation. Source data are provided as a Source Data file.