a, Ex vivo IFNγ ELISPOT observed in a patient treated with dexamethasone during vaccine priming (patient 4, left) showed no response at 12 weeks after vaccination, whereas a patient who did not receive dexamethasone (patient 8, right) showed strong response already at 8 weeks after vaccination. DMSO, dimethyl sulfoxide; CEF, peptides from cytomegalovirus, Epstein–Barr virus and influenza virus. b, Deconvolution of post-vaccination CD4+ and CD8+ immune responses following stimulation to the neoantigen assay peptide pools using IFNγ ELISPOT assays. n = 3 biologically independent samples, data are mean ± s.d. c, SLX4MUT and ARHGAP35MUT CD8+ T cell responses are only detected by ELISPOT assay in samples 16 weeks after vaccination, not pre-vaccination samples after stimulation in vitro for three weeks. Control, DMSO. d, Representative IFNγ ELISPOT responses from dominant neoantigen-specific T cell lines established from week 8 or week 16 PBMCs of vaccinated patients against minigene (MG)-transfected patient B cells, demonstrating epitope processing and presentation; ELISPOT experiments were performed in triplicate wells per time point. e, Analysis of ex vivo T cell responses to neoantigen assay peptide pools using intracellular cytokine staining followed by flow cytometry. Data are representative of results from three independent experiments. PHA, phytohaemagglutinin. f, IL-2 producing pool A-reactive T cells isolated ex vivo from patient 8 express CD45RO (memory) and PD-1 (activation) markers. Data are representative of results from two independent experiments.