Prediction of affinity between epitopes and HLA alleles

Using our TutuGenetics software [35], we were able to estimate the theoretical affinity between the putative epitopes and the HLA class I molecules of each patient. The TutuGenetics algorithm moves a sliding window of 8 to 10 amino acids across the test sequence and calculates the MHC IC₅₀ value according to each HLA allele of each patient to identify theoretically new HLA-epitope pairs. In order to identify potential epitopes with high binding affinity and conserved sequence across the available DNA sequence dataset, a conservative cut-off was applied so that only those epitopes with a theoretical MHC IC₅₀ < 50nm binding affinity and observed in >80% of all sequences analyzed were included.