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Objectives

  1. Provide highly qualified neoantigen selections for our patient cases.
  2. Report on output variation between pipelines.
  3. Evaluate the case for consortium-based neoantigen selection.

Neoantigen Analysis

  1. Individual neoantigen sets: prediction set (n~20) from each group.
  2. Gross neoantigen prediction lists.
  3. As a group, we will make a master composite list (n~20).

Immunogenicity Testing

We are evaluating to following options to test the 20 selected peptides.

  1. Peptide-MHC Binding Assays: measure ability of peptides to bind MHC class I molecules on cell surface or quantify binding affinity between peptide and soluble MHC proteins (Sette et al 2005) ProImmune offers this as a service
  2. Interferon (IFN)-γ ELISpot assay: measure T cell cytokine secretion (Charneau et al, Braun, )
  3. IFNg Intracellular Staining Assays (Flow Cytometry)
  4. Neoantigen T cell expansion: longer and more laborious, 7-10 days. (Sahin et al, 2017)

Expectations

  1. Each participating group submits a gross and ranked list of neoantigens for our patient datasets.
  2. Submissions remain confidential.
  3. Consortium participants will be included in publication in the **Research to the People Journal.**

Timeline

Please submit neoantigen ranked list by early August 2025.

*By requesting to join, you will be added to our mailing list.