Fig. 1

Workflow overview a Overview of the recurrent neo-epitope candidates generation process: TCGA studies are selected for at least 100 donors with clinical annotations. For each of these studies, recurrent strongly supported missense Single-Nucleotide Variants are collected. Neo-epitopes binding to 11 HLA-1 types are predicted, redundancy is removed from that set (see B) and strong binders are retained. b Example of epitope redundancy: the 18 amino-acids long sequence surrounding recurrent variant GLRA3:S274L generates 7 binding neo-epitopes for the type HLA-A*02:01. Our pipeline retains only the strongest predicted binder for a given variant and HLA-1 type pair (the first, with an IC₅₀ of 8.8 nM in the example). c Number of SNVs occuring in genes classified as Oncogenes or Tumor Suppressors by Vogelstein et al. [28], at various point of the variant selection and neo-epitope selection process