2018 SITC: Improving Neoantigen Identification for Therapeutic and Diagnostic Use in Immuno-Oncology Using Mass Spectrometry and Machine Learning

Neoantigens are increasingly critical in immuno-oncology as therapeutic targets for neoantigen-based personalized cancer vaccines (PCVs) and as potential biomarkers for immunotherapy response. However, the methods for identifying which neoepitopes are more likely to provoke an immune response remains an important challenge for improving both the effectiveness of PCVs and enabling the potential use of neoantigens as a biomarker in immunotherapy. Current MHC binding prediction algorithms are primarily trained using in vitro MHC binding data, which does not encompass proteasomal cleavage and transport, important factors for neoantigen presentation. Recent advances in immuno-affinity purification and mass spec technology makes it possible to identify processed cell surface MHC bound peptides in an in vivo setting, providing the opportunity for development of improved neoantigen prediction pipelines.