Extended Data Figure 5. Mapping of CD4+ and CD8+ T cell responses to individual ASP and EPT to the immunizing peptides (IMP) for all 6 patients.
ASP and EPT covering the immunizing peptides are shown for the IMP that induced T cell responses. T cells from week 16 PBMCs were tested. Red bold and shading – to indicate mutated amino acid; absent in those IMPs arising from neoORFs. Blue underline – for class I epitopes, predicted epitopes (IC50< 300nM) based on NetMHCpan36,44; for class II epitopes, predicted epitopes <10 percentile based on the IEDB-recommended consensus approach combining NN-align, SMM-align, and CombLib if allele predictions are available, otherwise NetMHCIIpan (Supplementary Information 6)44. Red font– peptides that generated an ex vivo CD4+ T cell responses; blue font– peptides that generated T cell response after 1 round of pre-stimulation with peptides, Triangle– ASP or EPT-specific T cells that also recognized a corresponding mutated minigene; *– T cell responses against minigenes that were blocked by pan anti- HLA-DR or anti-HLA class I blocking antibodies for CD4+ or CD8+ T cells, respectively.