1. A. B. C. D. Above median: 0244 03803 1120 22640 2472 Below median:
3549
4091
4810
6336
9445
9449 C. D.
Supplementary Figure 1. (A) Differences in mutation burden in four versus single-caller bioinformatic analysis. (B) Sample IDs that transition from below the median with single caller system, to above the median with 4-caller system and vice versa. (C) Mutation burden above the median (442.5) is associated with overall survival in pre-treatment tumor samples (Kaplan-Meier, log-rank test, p=0.01). (D) Mutation burden above the median (495) is not significantly associated with overall survival in post-treatment tumor samples (Kaplan-Meier, log-rank test, p=0.29).

2. A. C. B. D.
Supplementary Figure 2. (A) Similarity scores between samples and viral epitopes. Each box in the box plot represents a distribution of viral pathogen scores for each sample, where each point in the distribution is the maximum score for a given viral epitope. The bar plots below the graph show the mutation load for each sample. (B) Similarity scores between samples and non-viral epitopes. (C) Similarity scores between samples and viral epitopes using only expressed neoepitopes. (D) Similarity scores between samples and non-viral epitopes using only expressed neoepitopes.

3. A. B.
Supplementary Figure 3. (A) Deconvolution of immune infiltrates using RNA-Seq in samples collected prior to treatment and (B) those collected after treatment. Red denotes samples obtained from a lymph node.

4. Supplementary Figure 4. Interferon gamma and alpha gene sets showed the strongest enrichment signal in patients that benefitted from the therapy (Signal Strength column), where a majority of the genes in these sets were seen to participate in the signal (Tag % = # members in signal / # members).