Extended Data Fig. 10. Neoantigen-specific T-cell expansion of persistent mutations.

The MANAFEST assay was used to test pMANA-specific T-cell recognition. A collection of 58 neopeptides arising from 41 somatic persistent and loss-prone mutations, selected blindly with respect to pMANA status, were synthesized and tested in autologous T cell cultures from peripheral blood for patient CGLU310. A higher frequency of antigen-specific T-cell expansion was identified in neopeptides associated with persistent (green bars, 15 out of 48) vs loss-prone (red bar, 1 out of 10) mutations. T-cell clonotypes (as nucleotide sequence) and neopeptides are listed alongside the plane while the height of the bars indicates the abundance of TCR clones. A floor value of frequency of 0.08 informed by the values observed in the negative control condition was applied to TCR clonotypic abundances.