Extended Data Figure 4. Deconvolution of peptide pools to identify neoantigen-specific T cell responses ex vivo against individual 15–16mer ASP.

Deconvolution of T cell reactivity against individual ASP by ex vivo IFN-γ ELISPOT using the week 16 post-vaccination PBMCs, tested in duplicate wells per peptide (bars: SEM). Responses were scored positive (‘*’) if >55 SFC (spot forming cell) were detected and were at least 1.5 standard deviations (SD) over the DMSO control (> 3 SD over background for Pt. 5 and 6). a, Patient 3 deconvolution. Inset: examples of positive IMP/ASP sequences; red- ASP stimulating reactivity, boxed- the mutated aa. b, Deconvolution for all other patients. c, IFN-γ ELISPOT response of Patient 3 CIT-specific CD8⁺ T cell line from week 16 (7×10⁴ CD8⁺ T cells/well) against mutated (Mut) versus corresponding wildtype (WT) peptide across a range of concentrations (10pg/ml–10µg/ml) pulsed on 1×10⁴ T cell-depleted PBMCs (hereafter referred to as APCs)/well, tested in triplicate.