Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population (original) (raw)

Code availability

Software and codes used for this study are available from URLs or upon request to the authors.

Data availability

HLA data have been deposited at the National Bioscience Database Center (NBDC) Human Database (research ID: hum0114) as open data without any access restrictions. GWAS data and phenotype data of the BBJ individuals are available at the NBDC Human Database (research ID: hum0014).

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Acknowledgements

We thank T. Aoi for kind support of the study. This research was supported by the Tailor-Made Medical Treatment program (the BioBank Japan Project) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), the Japan Agency for Medical Research and Development (AMED), MEXT KAKENHI (221S0002), Bioinformatics Initiative of Osaka University Graduate School of Medicine, and Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University. Y.O. was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (15H05670, 15H05911 and 15K14429), AMED (18gm6010001h0003 and 18ek0410041h0002), Takeda Science Foundation, the Uehara Memorial Foundation, the Naito Foundation, Daiichi Sankyo Foundation of Life Science, Senri Life Science Foundation and Suzuken Memorial Foundation. K.H. was supported by JSPS KAKENHI grant no. P16H06502 ‘Neo-self’. J.H. is an employee of Teijin Pharma Limited. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.

Author information

Authors and Affiliations

  1. Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
    Jun Hirata, Saori Sakaue, Masahiro Kanai, Ken Suzuki, Toshihiro Kishikawa, Kotaro Ogawa, Tatsuo Masuda, Kenichi Yamamoto & Yukinori Okada
  2. Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Hino, Japan
    Jun Hirata
  3. Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan
    Kazuyoshi Hosomichi
  4. Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
    Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Ken Suzuki, Masato Akiyama, Yoichiro Kamatani & Yukinori Okada
  5. Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
    Saori Sakaue
  6. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
    Masahiro Kanai
  7. Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
    Hirofumi Nakaoka & Ituro Inoue
  8. Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Ken Suzuki
  9. Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
    Masato Akiyama
  10. Department of Otorhinolaryngology, Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
    Toshihiro Kishikawa
  11. Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
    Kotaro Ogawa
  12. Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Osaka, Japan
    Tatsuo Masuda
  13. Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
    Kenichi Yamamoto
  14. Laboratory of Genome Technology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    Makoto Hirata
  15. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
    Koichi Matsuda
  16. Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
    Yukihide Momozawa
  17. RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
    Michiaki Kubo
  18. Kyoto-McGill International Collaborative School in Genomic Medicine, Sakyo-ku, Kyoto, Japan
    Yoichiro Kamatani
  19. Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
    Yukinori Okada

Authors

  1. Jun Hirata
  2. Kazuyoshi Hosomichi
  3. Saori Sakaue
  4. Masahiro Kanai
  5. Hirofumi Nakaoka
  6. Kazuyoshi Ishigaki
  7. Ken Suzuki
  8. Masato Akiyama
  9. Toshihiro Kishikawa
  10. Kotaro Ogawa
  11. Tatsuo Masuda
  12. Kenichi Yamamoto
  13. Makoto Hirata
  14. Koichi Matsuda
  15. Yukihide Momozawa
  16. Ituro Inoue
  17. Michiaki Kubo
  18. Yoichiro Kamatani
  19. Yukinori Okada

Contributions

Y.O. supervised the study. J.H., K.H., Y.K. and Y.O. wrote the manuscript. J.H., K.H., S.S., M. Kanai, K.I., K.S., M.A., T.K., K.O., T.M., K.Y., Y.K. and Y.O. conducted data analysis. M.H., K.M., M. Kubo and Y.K. provided data. Y.O., K.M. and M. Kubo collected samples. Y.O., K.H., H.N., Y.M. and I.I. conducted experiments.

Corresponding author

Correspondence toYukinori Okada.

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Hirata, J., Hosomichi, K., Sakaue, S. et al. Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population.Nat Genet 51, 470–480 (2019). https://doi.org/10.1038/s41588-018-0336-0

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