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Hum Genome Var. 2019 Jun 19;6:29. doi: 10.1038/s41439-019-0061-y. eCollection 2019.

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

Author information

1Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi Japan.
2Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi Japan.
3The University of Tokyo, Bunkyo-ku, Tokyo Japan.
4Toyama Genome Medical Science Project, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo Japan.
5Graduate School of Medicine, Tohoku University, Sendai, Miyagi Japan.
6Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Sakyo-ku, Kyoto Japan.
7Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo Japan.


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.


Data publication and archiving; Next-generation sequencing

Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

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