Extended Data Figure 5. Peptide-MHC tetramer T-cell responses against predicted HLA-A2 neoantigens.

HLA-A2 restricted neoantigens were predicted for 8 patients. Peptide-MHC tetramers were synthesized for 108 predicted HLA-A2 neoantigens. Patient peripheral blood cells were pre-treated with dasatinib and then stained with each tetramer. (a) To enable a more accurate estimation of background staining, patienT-cells were mixed and co-stained with fluorescently-barcoded cells from 2 or 3 healthy donors. A representative reaction with multiplexing of 3 healthy donors using cytomegalovirus peptide-MHC tetramer is shown. (b) Frequency of neoantigen specific CD8 T-cells from peripheral blood T-cells is shown (closed circles). The frequency of neoantigen-specific T-cells from healthy donor PBMCs for each neoantigen is also shown (open squares). Staining of a CMV peptide-MHC tetramer for each patient is shown in red. (c) Representative results for 3 viral peptides derived from HIV, influenza A (flu), and CMV are shown along with patient-specific neoantigen staining. The neoantigen SLC9C2 tetramer is shown as an example of a tetramer with high background staining of both patient and healthy donor CD8 cells.