PMID- 30692682
OWN - NLM
STAT- MEDLINE
DCOM- 20190424
LR  - 20221207
IS  - 1546-1718 (Electronic)
IS  - 1061-4036 (Linking)
VI  - 51
IP  - 3
DP  - 2019 Mar
TI  - Genetic and phenotypic landscape of the major histocompatibilty complex region in 
      the Japanese population.
PG  - 470-480
LID - 10.1038/s41588-018-0336-0 [doi]
AB  - To perform detailed fine-mapping of the major-histocompatibility-complex region, 
      we conducted next-generation sequencing (NGS)-based typing of the 33 human 
      leukocyte antigen (HLA) genes in 1,120 individuals of Japanese ancestry, 
      providing a high-resolution allele catalog and linkage-disequilibrium structure 
      of both classical and nonclassical HLA genes. Together with population-specific 
      deep-whole-genome-sequencing data (n = 1,276), we conducted NGS-based HLA, 
      single-nucleotide-variant and indel imputation of large-scale 
      genome-wide-association-study data from 166,190 Japanese individuals. A 
      phenome-wide association study assessing 106 clinical phenotypes identified 
      abundant, significant genotype-phenotype associations across 52 phenotypes. 
      Fine-mapping highlighted multiple association patterns conferring independent 
      risks from classical HLA genes. Region-wide heritability estimates and 
      genetic-correlation network analysis elucidated the polygenic architecture shared 
      across the phenotypes.
FAU - Hirata, Jun
AU  - Hirata J
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Hino, 
      Japan.
FAU - Hosomichi, Kazuyoshi
AU  - Hosomichi K
AD  - Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive 
      Medical Sciences, Kanazawa University, Ishikawa, Japan.
FAU - Sakaue, Saori
AU  - Sakaue S
AUID- ORCID: 0000-0003-3618-9717
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
AD  - Department of Allergy and Rheumatology, Graduate School of Medicine, the 
      University of Tokyo, Tokyo, Japan.
FAU - Kanai, Masahiro
AU  - Kanai M
AUID- ORCID: 0000-0001-5165-4408
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
AD  - Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
FAU - Nakaoka, Hirofumi
AU  - Nakaoka H
AD  - Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan.
FAU - Ishigaki, Kazuyoshi
AU  - Ishigaki K
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
FAU - Suzuki, Ken
AU  - Suzuki K
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
AD  - Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The 
      University of Tokyo, Tokyo, Japan.
FAU - Akiyama, Masato
AU  - Akiyama M
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
AD  - Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu 
      University, Fukuoka, Fukuoka, Japan.
FAU - Kishikawa, Toshihiro
AU  - Kishikawa T
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Department of Otorhinolaryngology, Head and Neck Surgery, Osaka University 
      Graduate School of Medicine, Osaka, Japan.
FAU - Ogawa, Kotaro
AU  - Ogawa K
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 
      Japan.
FAU - Masuda, Tatsuo
AU  - Masuda T
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Department of Obstetrics and Gynecology, Osaka University Graduate School of 
      Medicine, Osaka, Japan.
FAU - Yamamoto, Kenichi
AU  - Yamamoto K
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan.
AD  - Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, 
      Japan.
FAU - Hirata, Makoto
AU  - Hirata M
AUID- ORCID: 0000-0002-9994-9958
AD  - Laboratory of Genome Technology, Institute of Medical Science, The University of 
      Tokyo, Tokyo, Japan.
FAU - Matsuda, Koichi
AU  - Matsuda K
AUID- ORCID: 0000-0001-7292-2686
AD  - Department of Computational Biology and Medical Sciences, Graduate School of 
      Frontier Sciences, The University of Tokyo, Tokyo, Japan.
FAU - Momozawa, Yukihide
AU  - Momozawa Y
AD  - Laboratory for Genotyping Development, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
FAU - Inoue, Ituro
AU  - Inoue I
AD  - Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan.
FAU - Kubo, Michiaki
AU  - Kubo M
AD  - RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
FAU - Kamatani, Yoichiro
AU  - Kamatani Y
AUID- ORCID: 0000-0001-8748-5597
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan.
AD  - Kyoto-McGill International Collaborative School in Genomic Medicine, Sakyo-ku, 
      Kyoto, Japan.
FAU - Okada, Yukinori
AU  - Okada Y
AUID- ORCID: 0000-0002-0311-8472
AD  - Department of Statistical Genetics, Osaka University Graduate School of Medicine, 
      Suita, Japan. yokada@sg.med.osaka-u.ac.jp.
AD  - Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical 
      Sciences, Yokohama, Japan. yokada@sg.med.osaka-u.ac.jp.
AD  - Laboratory of Statistical Immunology, Immunology Frontier Research Center 
      (WPI-IFReC), Osaka University, Suita, Japan. yokada@sg.med.osaka-u.ac.jp.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20190128
PL  - United States
TA  - Nat Genet
JT  - Nature genetics
JID - 9216904
SB  - IM
MH  - Alleles
MH  - Asian People/*genetics
MH  - Cell Line
MH  - Genetic Association Studies/methods
MH  - Genome-Wide Association Study/methods
MH  - Genotype
MH  - Humans
MH  - Linkage Disequilibrium/genetics
MH  - Major Histocompatibility Complex/*genetics
MH  - Phenotype
MH  - Polymorphism, Single Nucleotide/genetics
EDAT- 2019/01/30 06:00
MHDA- 2019/04/25 06:00
CRDT- 2019/01/30 06:00
PHST- 2018/02/27 00:00 [received]
PHST- 2018/12/13 00:00 [accepted]
PHST- 2019/01/30 06:00 [pubmed]
PHST- 2019/04/25 06:00 [medline]
PHST- 2019/01/30 06:00 [entrez]
AID - 10.1038/s41588-018-0336-0 [pii]
AID - 10.1038/s41588-018-0336-0 [doi]
PST - ppublish
SO  - Nat Genet. 2019 Mar;51(3):470-480. doi: 10.1038/s41588-018-0336-0. Epub 2019 Jan 
      28.