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Lookup NU author(s): Emeritus Professor John Robinson
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
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.
Author(s): Boelen L, O'Neill PK, Quigley KJ, Reynolds CJ, Maillere B, Robinson JH, Lertmemongkolchai G, Altmann DM, Boyton RJ, Asquith B
Publication type: Article
Publication status: Published
Journal: PLoS Computational Biology
Year: 2016
Volume: 12
Issue: 3
Online publication date: 08/03/2016
Acceptance date: 08/02/2016
Date deposited: 21/07/2016
ISSN (print): 1553-734X
ISSN (electronic): 1553-7358
Publisher: Public Library of Science
URL: http://dx.doi.org/10.1371/journal.pcbi.1004796
DOI: 10.1371/journal.pcbi.1004796
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