Fig. 5

Receiver operating characteristic curves of predictive capacity of nine different variant/neoepitope burden metrics. The upper panels depict the true positive rate (sensitivity, y-axis) and false positive rate (1-specificity, x-axis) for each metric across all probability thresholds. The three panels represent models for three different cohorts based on different subsets of patients: All Cancers, which includes all patients, and Melanoma, and RCC, which include only melanoma and RCC patients, respectively. The table in the lower panel reports the area under the curve (AUC) for each metric (columns) applied to a different cancer cohort (rows), with colors above the methods indicating the color of the corresponding curve in the upper panels. TMB and TVB are used as predictors in the raw formats. Jx represents the number of tumor-specific junctions per patient, and RI represents the number of retained introns per patient, with RI epitopes representing neoepitopes derived from those retained introns. Neoepitope burden is used as predictor in its RNA-feature-extended formats (see “Methods”). Extended neoepitope burden metrics include number of expressed transcripts for each epitope (E), number of amino acid mismatches (M), number of HLA alleles predicted to bind each epitope (A), and number of transcripts expressing each epitope in TCGA (T), along with their multiplicative combinations