A pan-specific approach to MHC class I pathway predictions

Reverse immunogenetic approaches attempt to optimize the selection of candidate epitopes and thus minimize the experimental effort needed to identify new epitopes. Methods have been developed for predicting the major antigen processing steps including the highly specific MHC class I binding event, proteasomal cleavage and transporter associated with antigen processing (TAP) transport efficiency. During recent years, novel so-called pan-specific prediction algorithms have been developed allowing for prediction of peptide binding for all MHC class I molecules. This pan-specific approach has however not been attempted in the context of MHC class I pathway predictions. In this project, the NetMHCpan method will be integrated with prediction of proteasomal cleavage and TAP translocation, and the ability to identify CTL epitopes will be benchmarked against conventional single allele state-of-the-art class I pathway prediction algorithms.