Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.

Authors: Mimori, Takahiro and Yasuda, Jun and Kuroki, Yoko and Shibata, Tomoko F and Katsuoka, Fumiki and Saito, Sakae and Nariai, Naoki and Ono, Akira and Nakai-Inagaki, Naomi and Misawa, Kazuharu and Tateno, Keiko and Kawai, Yosuke and Fuse, Nobuo and Hozawa, Atsushi and Kuriyama, Shinichi and Sugawara, Junichi and Minegishi, Naoko and Suzuki, Kichiya and Kinoshita, Kengo and Nagasaki, Masao and Yamamoto, Masayuki

Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.

Journal: The Pharmacogenomics journal
DOI: 10.1038/s41397-017-0010-4
Year: 2019

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