Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations

The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the...

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Autores principales: Pierini, Federica, Nutsua, Marcel, Böhme, Lisa, Özer, Onur, Bonczarowska, Joanna, Susat, Julian, Franke, Andre, Nebel, Almut, Krause-Kyora, Ben, Lenz, Tobias L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
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Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193575/
https://www.ncbi.nlm.nih.gov/pubmed/32355290
http://dx.doi.org/10.1038/s41598-020-64312-w
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author Pierini, Federica
Nutsua, Marcel
Böhme, Lisa
Özer, Onur
Bonczarowska, Joanna
Susat, Julian
Franke, Andre
Nebel, Almut
Krause-Kyora, Ben
Lenz, Tobias L.
author_facet Pierini, Federica
Nutsua, Marcel
Böhme, Lisa
Özer, Onur
Bonczarowska, Joanna
Susat, Julian
Franke, Andre
Nebel, Almut
Krause-Kyora, Ben
Lenz, Tobias L.
author_sort Pierini, Federica
collection PubMed
description The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
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spelling pubmed-71935752020-05-08 Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations Pierini, Federica Nutsua, Marcel Böhme, Lisa Özer, Onur Bonczarowska, Joanna Susat, Julian Franke, Andre Nebel, Almut Krause-Kyora, Ben Lenz, Tobias L. Sci Rep Article The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations. Nature Publishing Group UK 2020-04-30 /pmc/articles/PMC7193575/ /pubmed/32355290 http://dx.doi.org/10.1038/s41598-020-64312-w Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Pierini, Federica
Nutsua, Marcel
Böhme, Lisa
Özer, Onur
Bonczarowska, Joanna
Susat, Julian
Franke, Andre
Nebel, Almut
Krause-Kyora, Ben
Lenz, Tobias L.
Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
title Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
title_full Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
title_fullStr Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
title_full_unstemmed Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
title_short Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations
title_sort targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of hla genes in historical human populations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193575/
https://www.ncbi.nlm.nih.gov/pubmed/32355290
http://dx.doi.org/10.1038/s41598-020-64312-w
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