PMID- 29352165 OWN - NLM STAT- MEDLINE DCOM- 20190802 LR - 20200225 IS - 1473-1150 (Electronic) IS - 1470-269X (Print) IS - 1470-269X (Linking) VI - 19 IP - 2 DP - 2019 Apr TI - Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. PG - 136-146 LID - 10.1038/s41397-017-0010-4 [doi] AB - 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. FAU - Mimori, Takahiro AU - Mimori T AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Yasuda, Jun AU - Yasuda J AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. jyasuda@megabank.tohoku.ac.jp. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. jyasuda@megabank.tohoku.ac.jp. FAU - Kuroki, Yoko AU - Kuroki Y AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - National Research Institute for Child Health and Development, Tokyo, Japan. FAU - Shibata, Tomoko F AU - Shibata TF AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Katsuoka, Fumiki AU - Katsuoka F AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Saito, Sakae AU - Saito S AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Nariai, Naoki AU - Nariai N AD - Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, USA. FAU - Ono, Akira AU - Ono A AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. FAU - Nakai-Inagaki, Naomi AU - Nakai-Inagaki N AD - RIKEN Quantitative Biology Center, Osaka, Japan. FAU - Misawa, Kazuharu AU - Misawa K AUID- ORCID: 0000-0002-6277-4330 AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Tateno, Keiko AU - Tateno K AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. FAU - Kawai, Yosuke AU - Kawai Y AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. AD - Graduate School of Information Sciences, Tohoku University, Sendai, Japan. AD - Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. FAU - Fuse, Nobuo AU - Fuse N AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. AD - Tohoku University Hospital, Tohoku University, Sendai, Japan. FAU - Hozawa, Atsushi AU - Hozawa A AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Kuriyama, Shinichi AU - Kuriyama S AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. AD - International Research Institute of Disaster Science, Tohoku University, Sendai, Japan. FAU - Sugawara, Junichi AU - Sugawara J AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. AD - Tohoku University Hospital, Tohoku University, Sendai, Japan. FAU - Minegishi, Naoko AU - Minegishi N AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. FAU - Suzuki, Kichiya AU - Suzuki K AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. AD - Tohoku University Hospital, Tohoku University, Sendai, Japan. FAU - Kinoshita, Kengo AU - Kinoshita K AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Information Sciences, Tohoku University, Sendai, Japan. FAU - Nagasaki, Masao AU - Nagasaki M AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. nagasaki@megabank.tohoku.ac.jp. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. nagasaki@megabank.tohoku.ac.jp. AD - Graduate School of Information Sciences, Tohoku University, Sendai, Japan. nagasaki@megabank.tohoku.ac.jp. FAU - Yamamoto, Masayuki AU - Yamamoto M AD - Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. AD - Graduate School of Medicine, Tohoku University, Sendai, Japan. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20180119 PL - United States TA - Pharmacogenomics J JT - The pharmacogenomics journal JID - 101083949 RN - 0 (Histocompatibility Antigens Class I) MH - Alleles MH - *Genetic Variation MH - Genome, Human/*genetics MH - Genotype MH - *High-Throughput Nucleotide Sequencing MH - Histocompatibility Antigens Class I/*genetics MH - Histocompatibility Testing MH - Humans MH - Japan MH - Sequence Analysis, DNA PMC - PMC6462828 COIS- The authors declare that they have no conflict of interest. EDAT- 2018/01/21 06:00 MHDA- 2019/08/03 06:00 PMCR- 2018/01/19 CRDT- 2018/01/21 06:00 PHST- 2017/06/15 00:00 [received] PHST- 2017/11/06 00:00 [accepted] PHST- 2017/10/11 00:00 [revised] PHST- 2018/01/21 06:00 [pubmed] PHST- 2019/08/03 06:00 [medline] PHST- 2018/01/21 06:00 [entrez] PHST- 2018/01/19 00:00 [pmc-release] AID - 10.1038/s41397-017-0010-4 [pii] AID - 10 [pii] AID - 10.1038/s41397-017-0010-4 [doi] PST - ppublish SO - Pharmacogenomics J. 2019 Apr;19(2):136-146. doi: 10.1038/s41397-017-0010-4. Epub 2018 Jan 19.