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Objectives

1. Provide highly qualified neoantigen selections for our patient cases.
2. Measure how target selection has improved in 5 years since the PICI benchmark.
3. Re-examine / build on the case for consortium-based neoantigen selection.

Neoantigen Rankings

1. Individual neoantigen sets: prediction set (n~30) from each group.
2. Composite prediction set (n~30) from random pairings of 2-3 Groups.
3. Master Composite set (n~30) from all groups.
4. Overall: All neoantigens tested and ranked.

Immunogenicity

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 list of (n) ranked neoantigens for 2-3 patient datasets.
2. Submissions remain confidential.
3. Consortium participants will be included in publication.

Timeline

Start: April 15th, 2025

Mid-Point: June 15th, 2025

Finish: August 15th, 2025