Fig. 1: Sensitive tumor antigen discovery.
From: Sensitive identification of neoantigens and cognate TCRs in human solid tumors
a, NeoScreen pipeline. b–e, Antigen discovery with NeoScreen (n = 7 patients). b,c, Representative examples of flow cytometry data (b) and cumulative frequencies (c) of tumor antigen-specific CD8 T cells (n = 19 epitopes) in conventional (x axis) and NeoScreen (y axis) TIL cultures, by pMHC-multimers or 4-1BB upregulation. d, Proportions of neoepitope- versus TAA-specific among enriched versus newly detected T cell reactivities. e, Number of tumor epitopes per patient identified with conventional and NeoScreen strategies (histograms report median values). f, Frequencies of tumor antigen-specific CD8 T cells (n = 23 epitopes from nine patients) in conventional (x axis) and NeoScreen (y axis) cultures. g, Frequencies of antigen-specific CD8 T cells (n = 23) in in vitro expanded TIL cultures (2×: re-stimulated). Box plots represent the median (line), 25% and 75% confidence limit (box limits) and min to max (whiskers). In c,f and g, the background levels of 4-1BB expressed by cognate negative controls were subtracted. In c and f, the highest values between 1×NeoScreen and 2×NeoScreen are considered, and data are displayed in logarithmic scale. In c and e–g, P values were determined with one-tailed paired t-tests.
