title: Overlap of the cancer genome atlas and the immune epitope database.
abstract: Mutant peptides resulting from cancer drivers or passenger mutations are expected to have the potential to serve as a basis for cancer vaccines. However, a number of parameters regulate vaccine-associated immunogenicity, including the suitability of a peptide for binding to an antigen-presenting molecule or antibody. In order to obtain a basic indication of the prospect of human cancer epitope identification via current database development strategies, an overlap of the mutantHomo sapiensepitopes listed on the Immune Epitope Database (IEDB) and the mutant peptides indicated by The Cancer Genome Atlas (TCGA) somatic mutation database was obtained. No putative TCGA mutant peptides were detected among the 8,890 14-18 amino acid (AA) IEDB peptides available. In total, 3 IEDB mutant epitopes that encompassed a TCGA mutant AA position, but did not overlap the exact position of the TCGA mutant AA, were detected. The results of the present analysis confirm that verification of certain aspects of cancer epitope function can be obtained via the continued and systematic expansion of databases representing human protein epitopes. However, the analysis also indicates that there is relatively limited systematic information available regarding antigen-presenting molecule epitopes and cancer-related mutant peptides.
authors.affiliation: Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL 33612, USA.
authors.forename: Shaimaa
authors.initials: S
authors.lastname: Sait
authors.affiliation: Department of Chemical and Biomedical Engineering, College of Engineering, Research Computing University of South Florida, Tampa, FL 33620, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Fawcett
authors.affiliation: Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL 33612, USA; Immunology Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
authors.forename: George
authors.initials: G
authors.lastname: Blanck
keywords: Immune Epitope Database; The Cancer Genome Atlas; bioinformatics; cancer immunology; collagen type II α 1; extra-cellular matrix proteins; immuno-peptidome project; integrin subunit β 3