HLA isogenotypic virtual patient analysis.

(A) Somatic driver mutations were simulated in a set of virtual patients, each characterized by the same prototypical MHC-I and MHC-II genotype. (B-C) Box plots comparing MHC-I (B) and MHC-II (C) PHBR values between observed (+) and unobserved (-) mutations. (D) Scatter plot showing correlation between mutation frequency and MHC-I PHBR values. Thirteen weak HLA affinity mutations, as identified in Fig 3, are highlighted in red and labelled. Loess regression line shown in red. Median PHBR value from all driver mutations indicated by dashed line. (E-F) Box plots comparing MHC-I (E) and MHC-II (F) PHBR values for 10/30/100 most frequent mutations as indicated. Box plots indicate median values and lower/upper quartiles with whiskers extending to 1.5 times the interquartile range. P values calculated using Wilcoxon rank-sum test.