title: Automatic Generation of Validated Specific Epitope Sets.
abstract: Accurate measurement of B and T cell responses is a valuable tool to study autoimmunity, allergies, immunity to pathogens, and host-pathogen interactions and assist in the design and evaluation of T cell vaccines and immunotherapies. In this context, it is desirable to elucidate a method to select validated reference sets of epitopes to allow detection of T and B cells. However, the ever-growing information contained in the Immune Epitope Database (IEDB) and the differences in quality and subjects studied between epitope assays make this task complicated. In this study, we develop a novel method to automatically select reference epitope sets according to a categorization system employed by the IEDB. From the sets generated, three epitope sets (EBV, mycobacteria and dengue) were experimentally validated by detection of T cell reactivity ex vivo from human donors. Furthermore, a web application that will potentially be implemented in the IEDB was created to allow users the capacity to generate customized epitope sets.
authors.affiliation: Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru ; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Carrasco Pro
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: John
authors.initials: J
authors.lastname: Sidney
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Sinu
authors.initials: S
authors.lastname: Paul
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Lindestam Arlehamn
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Daniela
authors.initials: D
authors.lastname: Weiskopf
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Bjoern
authors.initials: B
authors.lastname: Peters
authors.affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sette
mesh_terms: D002478:Cells, Cultured; D016208:Databases, Factual; D003716:Dengue Virus / Q000276:immunology*; D001330:Electronic Data Processing; D018604:Epitope Mapping / Q000379:methods; D018984:Epitopes, T-Lymphocyte / Q000378:metabolism*; D004854:Herpesvirus 4, Human / Q000276:immunology*; D006801:Humans; D007159:Immunologic Tests; D007167:Immunotherapy; D008213:Lymphocyte Activation; D009159:Mycobacteriaceae / Q000276:immunology*; D057285:Precision Medicine; D012984:Software; D013601:T-Lymphocytes / Q000276:immunology*; D014764:Viral Proteins / Q000276:immunology*
chemical_list: D018984:Epitopes, T-Lymphocyte; D014764:Viral Proteins