Extended Data Fig. 4: T cell reactivity analysis and TCRseq tissue profiling.
From: Clonal driver neoantigen loss under EGFR TKI and immune selection pressures
a, Workflow for immunoreactivity assays. b, IFN-gamma Fluorospot at month 40; bars represent the mean +/− SEM of triplicate cultures; *P < 0.0001, one-way ANOVA. c, MANAFEST results showing significant clones in the conditions/time points indicated. d, MANAFEST parameters were adjusted over a sliding scale of expansion level for CDR3B sequences to be included in analysis (template threshold). Data show that post vaccine samples (months 40, 45) consistently harboured increased EGFR peptide reactivity relative to pre-vaccine timepoints (Month 30), irrespective of the template threshold used. In all analyses, clones enriched versus the cytokine alone sample and present at significantly higher levels in one condition vs all other conditions (OR > 10 and FDR < 0.01) by Fisher’s exact test, are classified as specific. e, TCRseq libraries of biopsies from 19 months (right upper lobe) and 38 months (liver metastasis), showing all significant CDR3s from MANAFEST assays. CEF = CMV, EBV, Flu viral pools of peptides. Illustration in a was created using BioRender (https://biorender.com).
