HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel

HLA-VBSeq is an HLA calling tool developed to infer the most likely HLA types from high-throughput sequencing data. However, there is still room for improvement in specific genetic groups because of the diversity of HLA alleles in human populations. Here, we present HLA-VBSeq v2, a software applicat...

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Autores principales: Wang, Yen-Yen, Mimori, Takahiro, Khor, Seik-Soon, Gervais, Olivier, Kawai, Yosuke, Hitomi, Yuki, Tokunaga, Katsushi, Nagasaki, Masao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Software Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584547/
https://www.ncbi.nlm.nih.gov/pubmed/31240105
http://dx.doi.org/10.1038/s41439-019-0061-y
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author Wang, Yen-Yen
Mimori, Takahiro
Khor, Seik-Soon
Gervais, Olivier
Kawai, Yosuke
Hitomi, Yuki
Tokunaga, Katsushi
Nagasaki, Masao
author_facet Wang, Yen-Yen
Mimori, Takahiro
Khor, Seik-Soon
Gervais, Olivier
Kawai, Yosuke
Hitomi, Yuki
Tokunaga, Katsushi
Nagasaki, Masao
author_sort Wang, Yen-Yen
collection PubMed
description HLA-VBSeq is an HLA calling tool developed to infer the most likely HLA types from high-throughput sequencing data. However, there is still room for improvement in specific genetic groups because of the diversity of HLA alleles in human populations. Here, we present HLA-VBSeq v2, a software application that makes use of a new Japanese HLA reference panel to enhance calling accuracy for Japanese HLA class-I genes. Our analysis showed significant improvements in calling accuracy in all HLA regions, with prediction accuracies achieving over 99.0, 97.8, and 99.8% in HLA-A, B and C, respectively.
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spelling pubmed-65845472019-06-25 HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel Wang, Yen-Yen Mimori, Takahiro Khor, Seik-Soon Gervais, Olivier Kawai, Yosuke Hitomi, Yuki Tokunaga, Katsushi Nagasaki, Masao Hum Genome Var Software Report HLA-VBSeq is an HLA calling tool developed to infer the most likely HLA types from high-throughput sequencing data. However, there is still room for improvement in specific genetic groups because of the diversity of HLA alleles in human populations. Here, we present HLA-VBSeq v2, a software application that makes use of a new Japanese HLA reference panel to enhance calling accuracy for Japanese HLA class-I genes. Our analysis showed significant improvements in calling accuracy in all HLA regions, with prediction accuracies achieving over 99.0, 97.8, and 99.8% in HLA-A, B and C, respectively. Nature Publishing Group UK 2019-06-19 /pmc/articles/PMC6584547/ /pubmed/31240105 http://dx.doi.org/10.1038/s41439-019-0061-y Text en © The Author(s) 2019 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 Software Report
Wang, Yen-Yen
Mimori, Takahiro
Khor, Seik-Soon
Gervais, Olivier
Kawai, Yosuke
Hitomi, Yuki
Tokunaga, Katsushi
Nagasaki, Masao
HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel
title HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel
title_full HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel
title_fullStr HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel
title_full_unstemmed HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel
title_short HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel
title_sort hla-vbseq v2: improved hla calling accuracy with full-length japanese class-i panel
topic Software Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584547/
https://www.ncbi.nlm.nih.gov/pubmed/31240105
http://dx.doi.org/10.1038/s41439-019-0061-y
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