title: BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data.
abstract: Activation of CD4+ T cells requires the recognition of peptides that are presented by HLA class II molecules and can be assessed experimentally using the ELISpot assay. However, even given an individual's HLA class II genotype, identifying which class II molecule is responsible for a positive ELISpot response to a given peptide is not trivial. The two main difficulties are the number of HLA class II molecules that can potentially be formed in a single individual (3-14) and the lack of clear peptide binding motifs for class II molecules. Here, we present a Bayesian framework to interpret ELISpot data (BIITE: Bayesian Immunogenicity Inference Tool for ELISpot); specifically BIITE identifies which HLA-II:peptide combination(s) are immunogenic based on cohort ELISpot data. We apply BIITE to two ELISpot datasets and explore the expected performance using simulations. We show this method can reach high accuracies, depending on the cohort size and the success rate of the ELISpot assay within the cohort.
authors.affiliation: Section of Immunology, Wright-Fleming Institute, School of Medicine, Imperial College London, London, United Kingdom.
authors.forename: Lies
authors.initials: L
authors.lastname: Boelen
authors.affiliation: Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America.
authors.forename: Patrick K
authors.initials: PK
authors.lastname: O'Neill
authors.affiliation: Lung Immunology Group, Section of Infectious Diseases and Immunity, Hammersmith Hospital, Department of Medicine, Imperial College London, London, United Kingdom.
authors.forename: Kathryn J
authors.initials: KJ
authors.lastname: Quigley
authors.affiliation: Lung Immunology Group, Section of Infectious Diseases and Immunity, Hammersmith Hospital, Department of Medicine, Imperial College London, London, United Kingdom.
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Reynolds
authors.affiliation: CEA-Saclay, Institute of Biology and Technologies, SIMOPRO, Labex LERMIT, Labex VRI, Gif Sur Yvette, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Maillere
authors.affiliation: Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.
authors.forename: John H
authors.initials: JH
authors.lastname: Robinson
authors.affiliation: Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
authors.forename: Ganjana
authors.initials: G
authors.lastname: Lertmemongkolchai
authors.affiliation: Lung Immunology Group, Section of Infectious Diseases and Immunity, Hammersmith Hospital, Department of Medicine, Imperial College London, London, United Kingdom.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Altmann
authors.affiliation: Lung Immunology Group, Section of Infectious Diseases and Immunity, Hammersmith Hospital, Department of Medicine, Imperial College London, London, United Kingdom.|Department of Respiratory Medicine, Royal Brompton & Harefield NHS Foundation Trust, Sydney Street, London, United Kingdom.
authors.forename: Rosemary J
authors.initials: RJ
authors.lastname: Boyton
authors.affiliation: Section of Immunology, Wright-Fleming Institute, School of Medicine, Imperial College London, London, United Kingdom.
authors.forename: Becca
authors.initials: B
authors.lastname: Asquith
mesh_terms: D000465:Algorithms; D016957:Burkholderia pseudomallei / Q000276:immunology; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D058501:Enzyme-Linked Immunospot Assay / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry* / Q000276:immunology*; D000949:Histocompatibility Antigens Class II / Q000737:chemistry* / Q000276:immunology*; D006801:Humans; D008554:Melioidosis / Q000276:immunology; D018448:Models, Immunological; D010455:Peptides / Q000032:analysis / Q000737:chemistry / Q000276:immunology; D012984:Software
chemical_list: D018984:Epitopes, T-Lymphocyte; D000949:Histocompatibility Antigens Class II; D010455:Peptides