Neoantigen immunotherapies

A method for treating cancer in a subject comprising designing a group of one or more tumor-specific T-cell stimulating peptides, or nucleic acids encoding T cell stimulating peptides, which have a desired predicted binding affinity for the MHC alleles of the subject, comprising the following steps:

• obtaining a biopsy of the subject's tumor;
• obtaining sequences for proteins in said biopsy;
• identifying proteins from the biopsy containing mutated amino acids and the peptide comprising each of said mutated amino acids;
• determining T cell exposed motifs which comprise mutated amino acids in each of the proteins;
• determining the predicted binding affinity to the subject's MHC alleles of peptides which comprises each of said T cell exposed motifs, or a subset thereof;
• generating an array of alternative peptides not present in the tumor, wherein each peptide in the array comprises the amino acids of one of said T cell exposed motifs, and in which one or more of the amino acids not within the T cell exposed motif are substituted to change the predicted MHC binding affinity;
• selecting a group of one or more selected peptides from said array of alternative peptides which have a desired predicted binding affinity for one or more of the subject's MHC alleles;
• and
• synthesizing said group of one or more selected peptides, or nucleic acids encoding the selected peptides.