A method for identifying T-cells that are antigen-specific forat least one neoantigen that is likely to be presented on surfaces of tumorcells of a subject. Peptide sequences of tumor neoantigens are obtained bysequencing the tumor cells of the subject. The peptide sequences are inputinto a machine-learned presentation model to generate presentationlikelihoods for the tumor neoantigens, each presentation likelihoodrepresentingthe likelihood that a neoantigen is presented by an MHC allele on thesurfaces of the tumor cells of the subject. A subset of the neoantigens isselectedbased on the presentation likelihoods. T-cells that are antigen-specific foratleast one of the neoantigens in the subset are identified. These T-cells canbe expanded for use in T-cell therapy. TCRs of these identified T-cells canalso be sequenced and cloned into new T-cells for use in T-cell therapy.
