Fig. 1

Overview of the bioinformatic characterization of neoantigens. Major analysis steps in a comprehensive workflow for neoantigen characterization are depicted in a simplified form. For each component, critical concepts and analysis considerations are indicated. Specific exemplar bioinformatics tools for each step are indicated in italics. Starting at the top left, patient sequences are analyzed to determine human leukocyte antigen (HLA) types and to predict the corresponding major histocompatibility complexes (MHC) for each tumor. Somatic variants of various types, including single nucleotide variants (SNVs; blue), deletions (red), insertions (green), and fusions (pink), are detected and the corresponding peptide sequences are analyzed with respect to their predicted expression, processing, and ability to bind the patient’s MHC complexes. Candidates are then selected for vaccine design and additional analyses are performed to assess the T cell response. Abbreviations: CDR3 complementarity-determining region 3, FFPE formalin-fixed paraffin-embedded, IEDB Immune Epitope Database, TCR T cell receptor