Fig. 3: High-quality neoantigens are immunoedited in LTS  PDACs.

a, Neoantigen quality model. b, The model and experimental approach to estimate cross-reactivity distance C. c, d, Measured (top) and fitted (bottom) p^MT–TCR activation curves (c, amino acid (AA) position 4), and activation heat maps (d, all amino acid positions) for stronger and weaker p^WT–TCR pairs. e, Composite p^MT–TCR EC₅₀ values of all stronger and weaker p^WT–TCR pairs. f, p^MT–TCR activation heat map and observed versus modelled C(p^WT, p^MT) for the HLA-B*27:05-restricted p^WT–TCR pair. n indicates the number of single-amino-acid-substituted p^WT, p^MT and p^MT, p^MT pairs. g, Cross-reactivity distance model C and dendrogram of agglomerative clustering of substitution matrix M. h, Observed amino acid substitution frequency versus matrix M-defined substitution distance in primary and recurrent STS and LTS PDACs. M distance is the matrix M-defined amino acid distance from g. Circles indicate substituted residues. n indicates the number of substitutions. i, Cumulative probability distributions of log(C) and D. n indicates the number of neoantigens. The red rectangles in the heat maps indicate amino acids in p^WT. The green line is a linear regression fit. Heat maps are ordered according to the amino acid order in the dendogram in g. P values were determined using two-tailed Pearson correlation (f and h) and two-sided Kolmogorov–Smirnov tests (i).

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