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

Yen-Yen Wang; Takahiro Mimori; Seik-Soon Khor; Olivier Gervais; Yosuke Kawai; Yuki Hitomi; Katsushi Tokunaga; Masao Nagasaki

doi:10.1038/s41439-019-0061-y

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

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

Authors

Yen-Yen Wang^{1

2}, Takahiro Mimori², Seik-Soon Khor^{3

4}, Olivier Gervais^{2

5

6}, Yosuke Kawai^{3

4}, Yuki Hitomi^{3

7}, Katsushi Tokunaga^{3

4}, Masao Nagasaki^{1

2

5

6}

Affiliations

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

Abstract

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.

Keywords: Data publication and archiving; Next-generation sequencing.