BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data.
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 E...
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| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-03-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1004796 |
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| author | Lies Boelen Patrick K O'Neill Kathryn J Quigley Catherine J Reynolds Bernard Maillere John H Robinson Ganjana Lertmemongkolchai Daniel M Altmann Rosemary J Boyton Becca Asquith |
| author_facet | Lies Boelen Patrick K O'Neill Kathryn J Quigley Catherine J Reynolds Bernard Maillere John H Robinson Ganjana Lertmemongkolchai Daniel M Altmann Rosemary J Boyton Becca Asquith |
| author_sort | Lies Boelen |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-bf41c06d42fd4022a66f3f8a1f57a94c |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2016-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-bf41c06d42fd4022a66f3f8a1f57a94c2025-08-20T02:34:09ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582016-03-01123e100479610.1371/journal.pcbi.1004796BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data.Lies BoelenPatrick K O'NeillKathryn J QuigleyCatherine J ReynoldsBernard MaillereJohn H RobinsonGanjana LertmemongkolchaiDaniel M AltmannRosemary J BoytonBecca AsquithActivation 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.https://doi.org/10.1371/journal.pcbi.1004796 |
| spellingShingle | Lies Boelen Patrick K O'Neill Kathryn J Quigley Catherine J Reynolds Bernard Maillere John H Robinson Ganjana Lertmemongkolchai Daniel M Altmann Rosemary J Boyton Becca Asquith BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data. PLoS Computational Biology |
| title | BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data. |
| title_full | BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data. |
| title_fullStr | BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data. |
| title_full_unstemmed | BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data. |
| title_short | BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data. |
| title_sort | biite a tool to determine hla class ii epitopes from t cell elispot data |
| url | https://doi.org/10.1371/journal.pcbi.1004796 |
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