Fig. 3

Robustness of putative neoepitope presentation. a The number of unique patient-matched HLA alleles that are predicted to present an individual neoepitope is shown along the x-axis, with the y-axis (log scale) corresponding to the overall percent of neoepitopes sharing that same robustness of HLA presentation. Red and blue curves denote the best fit line based on linear regression for all neoepitopes and those resulting from cancer driver mutations, respectively. The surrounding red and light blue shading denotes the 95% confidence interval for all and driver-derived neoepitopes, respectively. Individual data points are shown as open circles, whose diameter corresponds to the number of neoepitopes as shown by the corresponding scale at right. b The total number of unique patient-matched HLA alleles that are predicted to present one or more neoepitopes arising from a single DNA mutation is shown along the x-axis, with the y-axis corresponding to the overall percent of mutations sharing that same robustness of HLA presentation. Red and blue curves denote the best fit line based on local polynomial regression for all mutations and cancer driver mutations, respectively. The surrounding red and light blue shading denotes the 95% confidence interval for all and driver mutations, respectively. Individual data points are shown as open circles, whose diameter corresponds to the number of mutations as shown by the corresponding scale at right. c The percentage of total variants that are predicted to be presented by one or more patient-matched HLA alleles is shown along the y-axis, with the x-axis corresponding to the number of unique HLA alleles for that patient. Red and blue curves denote the best fit line based on linear regression for all mutations and cancer driver mutations, respectively. The surrounding red and light blue shading denotes the 95% confidence interval for all and driver mutations, respectively. Individual data points are shown as open circles, whose diameter corresponds to the number of mutations as shown by the corresponding scale at right. Note that a predicted HLA binding affinity threshold of ≤ 500 nM was used in all cases (see “Methods”)