The TILs present in an untreated tumor are different from those present in a tumor treated with checkpoint blockade or a personalized neoantigen vaccine.
To distinguish an incorrect epitope prediction from an epitope against which no immune response was mounted, it would be helpful to know the previous pathogen exposure and microbiome of the patient, as well as the capacity of their immune system to generate an immune response. It would also be helpful to know the immune contexture of the tumor, as a more immunosuppressive tumor microenvironment (TME) makes the possibility of no immune response more likely.
The proprietary T cell epitope discovery assay permits the phenotyping of T cells, so: perhaps. It would be useful to know if the T cells are activated, anergic, or exhausted.
We may selectively validate intermediate outputs such as predicted somatic mutations, HLA type, and peptide/MHC binding strength.