AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition

Abstract

Neoantigens—tumor-specific peptides generated by somatic mutations—are central targets of effective anticancer T cell immunity and underpin the clinical success of immune checkpoint blockade and personalized cancer vaccines. Advances in high-throughput sequencing, immunopeptidomics, and artificial intelligence (AI) have transformed neoantigen discovery from tailored experimental workflows into scalable, computational pipelines. However, accurately identifying the small subset of tumor mutations that yield processed, presented, and immunogenic epitopes remains a major bottleneck. This review summarizes how AI is reshaping neoantigen discovery, from somatic variant calling, HLA typing, and peptide processing to peptide–MHC binding, presentation, and T cell recognition. We first outline the immunobiological foundations of antigen presentation, emphasizing class I and II peptide-binding grooves and their allele-specific motifs, then describe AI workflows that integrate somatic mutation calling, HLA typing, transcriptomics, and immunopeptidomics to nominate candidate neoepitopes. We highlight recent AI-driven tools for presentation and immunogenicity prediction, integrative pipelines that support personal and shared neoantigen targeting, and early clinical applications in vaccination and T cell therapies. AI-driven models trained on eluted ligand datasets substantially outperform affinity-only predictors for peptide presentation across diverse HLA alleles and populations. Consortium-scale benchmarking demonstrates that integrating features of antigen processing, presentation, and TCR recognition can eliminate the majority of non-immunogenic candidates while retaining clinically relevant neoepitopes. Immunopeptidomics provides essential ground truth, revealing that only a small fraction of genomically predicted candidates are naturally presented and uncovering noncanonical antigen sources, including splice variants, post-translational modifications, and noncoding regions. Integrative pipelines now support both personal (private) and shared (public) neoantigen prioritization, enabling translational applications such as personalized vaccines and TCR-based therapies. AI-guided neoantigen discovery is now clinically actionable, enabled by immunopeptidomics and deep learning models. Despite significant progress, key challenges remain, including limited class II prediction accuracy, incomplete coverage of rare HLA alleles, tumor heterogeneity, and the need for standardized benchmarking and validation. Anchoring computational predictions to mass spectrometry–derived ligands and incorporating tumor evolution and immune escape mechanisms will be critical for improving target selection. Continued integration of AI, proteogenomics, and clinical data is poised to accelerate the development of effective, precision neoantigen-based cancer immunotherapies.