Extended Data Figure 5 |. Effect of IEDB sequence content on predictive power of neoantigen fitness model.

Predictions were performed using subsampled IEDB epitope sequences, with subsampling rate varying between 0.1 and 0.9. For each rate, 10,000 iterations were performed to obtain a distribution of log-rank test scores. The violin plots represent data density at a given value on a vertical axis (n=10,000). Solid black lines mark the log-rank test score of the prediction on the full set of epitope sequences and gray thick lines mark the median scores on subsampled data. a-c, Subsampling of the original set of IEDB sequences, supported by positive T-cell assays, shows that quality of predictions decreases with subsampling rate. Prediction quality is more robust in the Snyder et al. and Rizvi et al. datasets. d-f, Analogous subsampling procedure was repeated on IEDB sequences not supported by positive T-cell assays. For Van Allen et al. and Snyder et al. model performance is substantially lowered.