Fig. 5: Analysis of parallel evolution.
a, Spearman correlation (two-sided) between TMB and dN/dS in plasma at both baseline and relapse in the discovery cohort (left; n = 12) and the validation cohort (right; n = 15 participants). The P and ρ values are provided for each case. The line represents the fitted relationship between the variables, while the shaded band corresponds to the 95% confidence interval around the regression estimate. b, Volcano plot in the discovery cohort (left; n = 12 participants) and the validation cohort (right; n = 15 participants) illustrating genes significantly associated with a higher number of somatic mutations at relapse and baseline. The P-value threshold was set at 0.05 and the log2(fold change) range was between −0.6 and 0.6 (two-sided Wilcoxon test). The P values were adjusted for multiple comparisons using the FDR correction, with a significance threshold of 0.05. c, Functional enrichment analysis of all significant genes exhibiting a higher number of somatic mutations at relapse compared to the baseline stage in the discovery cohort (left; n = 12 participants) and the validation cohort (right; n = 15 participants). A one-sided hypergeometric test was used to assess whether the input gene set was significantly overrepresented in KEGG pathways compared to a background set of genes. The P values were adjusted for multiple comparisons using the FDR correction, with a significance threshold of 0.05. d, Comparative quantification of neoepitope abundance between paired metastatic and primary tumor samples (n = 13 participants). An asterisk denotes a statistically significant difference (P < 0.05) in neoepitope abundance between primary and metastatic tissues, as determined by a one-sided t-test. The analysis was based on the hypothesis that metastatic tissues exhibit a lower neoepitope abundance than primary tumors. The P value for the overall comparison between primary and metastatic tumors was <0.001. Individual P values for each participant were as follows: participant 13, 0.0132; participant 49, 0.0017; participant 63, 0.0068; participant 104, 0.0029; participant 107, 0.0219; participant 136, 0.9671; participant 185, 0.0001; participant 189, 0.8378; participant 204, 0.0001; participant 242, 0.0001; participant 243, 0.9945; participant 259, 0.0211; participant 261, 0.9997. e, Median protein quantification ratio of wild-type versus mutated metastasis samples identified by MS (n = 14 participants). The asterisk indicates a significant difference in protein ratio between primary and metastatic tissues based on the presence of the mutation at relapse according to a two-sided t-test analysis. Individual P values were as follows: PDIA3, 0.0014; HLA-A, 0.2091; HLA-B, 0.4807; HLA-C, 0.9548; HLA-DPB1, 0.6853; HLA-DQB1, 0.7936; HLA-DRB1, 0.0077; HLA-E, 0.2616; HSP90AA1, 0.7104; TAP1, 0.9010; CALR, 0.1663).
