HLA genotyping and neoantigen prediction
Major histocompatibility complex (MHC) allele typing was performed using Polysolver (v.1.0). netMHC (v.4.0), netMHCpan (v.4.1), MHCflurry (v.2.0.4), MixMHCpred (v.2.1) and HLAthena (v.1.0) were then integrated to evaluate affinity between class I MHCs and somatic peptides. Candidate neoantigens with an MHC affinity <500 nM were further selected to estimate the neoantigen-specific TCRs using a transfer learning-based model (pMTnet v.1.0.0). the pMTnet output was a percentile rank representing the potential binding strength between the TCR and somatic peptides with a smaller rank indicating a stronger binding possibility. Further analysis was performed using the top 2% binding ITC–neoantigen pairs.