Extended Data Fig. 3. Paired analysis of pre- and post-immune checkpoint blockade (ICB) exposed tumors using MSK-IMPACT next-generation sequencing derived data22.

Nonsynonymous somatic mutations from the MSK IMPACT variant call format (VCF) output from each sequenced patient tumor were input into the SnpEff program v5.1d (https://pcingola.github.io/SnpEff/) to predict translated amino acid sequences for each respective mutation. The number of unique mutation associated neoantigens (MANA) was determined by taking the defined peptide sequence and evaluating all potential contiguous 9′mer variations using a sliding reading frame. a, Comparison of total missense mutations in pre- and post-ICB tumors. b, Comparison of mutation associated neoantigens between pre- and post-ICB tumors. All boxplots are composed of median (central line), 25th–75th percentile (box edges), and minimum and maximum values (whiskers). All analyses included 9 distinct pre and 9 distinct post tumors paired for 9 unique patients. p-values are derived from pairwise t-testing based on patient.