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[…] eir allelic variants (p = 0.0005). Of the 45 pairs with polymorphic amino acids at TCR contact residues, 9 MiHA had predicted HLA class I binding affinities that were significantly higher than their allelic variants (p = 0.0039). In all these peptides, the polymorphic amino acid was located immediately adjacent to the N-terminal anchor residue at position 2. For the remaining 36 pairs, predicted HLA class I binding affinity was similar between MiHA and allelic variants (p = 0.1965)., Binding motifs as available at http://www.cbs.dtu.dk/biotools/MHCMotifViewer/Human_alleles.html []., We also compared MiHA and their allelic variants in predicted stability of the peptide-HLA class I complex by NetMHCstab 1.0 (). HLA class I restriction alleles were available for 41 pairs of MiHA and allelic variants. For 7 pairs with polymorphic amino acids at anchor residues, predicted stability of the peptide-HLA class I complex was significantly higher for MiHA than for their allelic variants (p = 0.0156), while predicted stability was similar for the majority of 34 pairs with polymorphic amino acids at TCR contact residues (p = 0.0781)., Finally, 57 pairs of MiHA and allelic variants were compared for predicted proteasomal cleavage, TAP affinity and in vivo immunogenicity (). No difference was observed in predicted proteasomal cleavage by NetChop 3.1 (81% for MiHA versus 81% for allelic variants, p = 1.000) and TAP affinity by TAPPred (40% high, 53% intermediate and 8% low affinity peptides for MiHA versus 47% high, 43% intermediate and 9% low affinity peptides for allelic variants). Moreover, immunogenicity scores as determined by the online tool of the IEDB were similar between MiHA (range between -0.42 and 0.42 with a median score of 0.09) and allelic variants (range between -0.54 and 0.46 with a median score of 0.05) (p = 0.2871). When a threshold of >0.25 was applied to define immunogenic peptides, 8 (14%) MiHA and 10 (18%) allelic variants were predicted to be immunogenic, including 5 pairs of MiHA and allelic variants for HLA-B*07:02., In conclusion, the data show that predicted HLA class I binding affin […]

Pipeline specifications

Software tools NetMHCstab, NetChop, TAPPred
Organisms Homo sapiens
Diseases Neoplasms, Hematologic Neoplasms