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

Pierini, F., Nutsua, M., Böhme, L., Özer, O., Bonczarowska, J., Susat, J., et al. (2020). Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations. Scientific Reports, 10: 7339. doi:10.1038/s41598-020-64312-w.

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 Creators:
Pierini, Federica1, 2, Author              
Nutsua, Marcel, Author
Böhme, Lisa, Author
Özer, Onur1, 2, Author              
Bonczarowska, Joanna, Author
Susat, Julian, Author
Franke, Andre, Author
Nebel, Almut, Author
Krause-Kyora, Ben, Author              
Lenz, Tobias L.2, Author              
Affiliations:
1IMPRS for Evolutionary Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445639              
2Emmy Noether Research Group Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2616693              

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 Abstract: 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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Language(s): eng - English
 Dates: 2019-12-122020-04-142020-04-30
 Publication Status: Published online
 Pages: -
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 Rev. Type: -
 Identifiers: DOI: 10.1038/s41598-020-64312-w
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Title: Scientific Reports
  Abbreviation : Sci. Rep.
Source Genre: Journal
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Publ. Info: London, UK : Nature Publishing Group
Pages: - Volume / Issue: 10 Sequence Number: 7339 Start / End Page: - Identifier: ISSN: 2045-2322
CoNE: https://pure.mpg.de/cone/journals/resource/2045-2322