Table 1 Advantages and disadvantages of different high-throughput strategies used for identification
From: Neoantigens and their clinical applications in human gastrointestinal cancers
Strategy | Advantages | Disadvantages |
|---|---|---|
Whole exome sequencing | Identification of all candidate neoantigens Fast and high-throughput | Minimal epitope is not defined Limited feasibility in tumors with high mutation burden No information on epitope presentation and immunogenicity |
Mass spectrometry | Narrows down the number of candidate neoantigens Allows the identification of post-translational modified peptides and non-canonical neoantigens Identification of minimal epitopes Identification of naturally HLA-presented antigens | Require sophisticated equipment Low sensitivity Biased toward detecting the more abundant peptides Depends on HLA expression of tumor cells Relies on efficient peptide ionization and fragmentation High amount of tumor tissue needed |
In silico predictions | Narrows down the number of candidate neoantigens Easily accessible Identification of minimal epitopes | Prediction tools are not always accurate, in particular for HLAs with low frequency Not optimal for HLA-II-presented peptides Depends on accuracy of prediction algorithms |
T cell assay | High versatility and throughput | Highly dependent on phenotype False negative Direct detection of T cell-recognized neoantigens |
Engineered APCs | Functional readout Physiological neoantigen presentation | Dependency on predefined antigen library |
Trogocytosis | Simultaneously identification of TCR and neoantigens | Lack of functional readout Dependency on predefined antigen library |
pMHC yeast library | Directly identification of TCR and precisely target of neoantigen | Lacks functional readout and neglects endogenous antigen processing |