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Development of a high-resolution NGS-based HLA-typing and analysis pipeline

The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases an...

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Autores principales: Wittig, Michael, Anmarkrud, Jarl A., Kässens, Jan C., Koch, Simon, Forster, Michael, Ellinghaus, Eva, Hov, Johannes R., Sauer, Sascha, Schimmler, Manfred, Ziemann, Malte, Görg, Siegfried, Jacob, Frank, Karlsen, Tom H., Franke, Andre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477639/
https://www.ncbi.nlm.nih.gov/pubmed/25753671
http://dx.doi.org/10.1093/nar/gkv184
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author Wittig, Michael
Anmarkrud, Jarl A.
Kässens, Jan C.
Koch, Simon
Forster, Michael
Ellinghaus, Eva
Hov, Johannes R.
Sauer, Sascha
Schimmler, Manfred
Ziemann, Malte
Görg, Siegfried
Jacob, Frank
Karlsen, Tom H.
Franke, Andre
author_facet Wittig, Michael
Anmarkrud, Jarl A.
Kässens, Jan C.
Koch, Simon
Forster, Michael
Ellinghaus, Eva
Hov, Johannes R.
Sauer, Sascha
Schimmler, Manfred
Ziemann, Malte
Görg, Siegfried
Jacob, Frank
Karlsen, Tom H.
Franke, Andre
author_sort Wittig, Michael
collection PubMed
description The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions.
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spelling pubmed-44776392015-06-29 Development of a high-resolution NGS-based HLA-typing and analysis pipeline Wittig, Michael Anmarkrud, Jarl A. Kässens, Jan C. Koch, Simon Forster, Michael Ellinghaus, Eva Hov, Johannes R. Sauer, Sascha Schimmler, Manfred Ziemann, Malte Görg, Siegfried Jacob, Frank Karlsen, Tom H. Franke, Andre Nucleic Acids Res Methods Online The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions. Oxford University Press 2015-06-23 2015-03-09 /pmc/articles/PMC4477639/ /pubmed/25753671 http://dx.doi.org/10.1093/nar/gkv184 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Wittig, Michael
Anmarkrud, Jarl A.
Kässens, Jan C.
Koch, Simon
Forster, Michael
Ellinghaus, Eva
Hov, Johannes R.
Sauer, Sascha
Schimmler, Manfred
Ziemann, Malte
Görg, Siegfried
Jacob, Frank
Karlsen, Tom H.
Franke, Andre
Development of a high-resolution NGS-based HLA-typing and analysis pipeline
title Development of a high-resolution NGS-based HLA-typing and analysis pipeline
title_full Development of a high-resolution NGS-based HLA-typing and analysis pipeline
title_fullStr Development of a high-resolution NGS-based HLA-typing and analysis pipeline
title_full_unstemmed Development of a high-resolution NGS-based HLA-typing and analysis pipeline
title_short Development of a high-resolution NGS-based HLA-typing and analysis pipeline
title_sort development of a high-resolution ngs-based hla-typing and analysis pipeline
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477639/
https://www.ncbi.nlm.nih.gov/pubmed/25753671
http://dx.doi.org/10.1093/nar/gkv184
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