Abstract

Japan Pharmacogenomics Data Science Consortium (JPDSC) has assembled a database for conducting pharmacogenomics (PGx) studies in Japanese subjects. The database contains the genotypes of 2.5 million single-nucleotide polymorphisms (SNPs) and 5 human leukocyte antigen loci from 2994 Japanese healthy volunteers, as well as 121 kinds of clinical information, including self-reports, physiological data, hematological data and biochemical data. In this article, the reliability of our data was evaluated by principal component analysis (PCA) and association analysis for hematological and biochemical traits by using genome-wide SNP data. PCA of the SNPs showed that all the samples were collected from the Japanese population and that the samples were separated into two major clusters by birthplace, Okinawa and other than Okinawa, as had been previously reported. Among 87 SNPs that have been reported to be associated with 18 hematological and biochemical traits in genome-wide association studies (GWAS), the associations of 56 SNPs were replicated using our data base. Statistical power simulations showed that the sample size of the JPDSC control database is large enough to detect genetic markers having a relatively strong association even when the case sample size is small. The JPDSC database will be useful as control data for conducting PGx studies to explore genetic markers to improve the safety and efficacy of drugs either during clinical development or in post-marketing.

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Acknowledgements

We thank all the study participants for making this study possible. We thank for the data kindly provided by the Japan Pharmacogenomics Data Science Consortium (JPDSC), which is composed of Astellas Pharma, Otsuka Pharmaceutical, Daiichi-Sankyo, Taisho Pharmaceutical, Takeda Pharmaceutical and Mitsubishi Tanabe Pharma Corporation, and is chaired by Dr Ichiro Nakaoka (Takeda Pharmaceutical).

Author information

Affiliations

  1. StaGen, Tokyo, Japan

    • Shigeo Kamitsuji
    • , Kazuyuki Nakazono
    • , Yuki Sugaya
    • , Woosung Yang
    •  & Naoyuki Kamatani
  2. Astellas Pharma, Tokyo, Japan

    • Takashi Matsuda
    • , Koichi Nishimura
    • , Taiji Sawamoto
    •  & Wataru Uchida
  3. Daiichi Sankyo, Tokyo, Japan

    • Seiko Endo
    • , Chisa Wada
    • , Kenji Watanabe
    •  & Akira Shinagawa
  4. Otsuka Pharmaceutical, Tokyo, Japan

    • Koichi Hasegawa
    • , Haretsugu Hishigaki
    • , Masatoshi Masuda
    •  & Tsutomu Fujiwara
  5. Taisho Pharmaceutical, Tokyo, Japan

    • Yusuke Kuwahara
    • , Katsuki Tsuritani
    • , Hisaharu Yamada
    •  & Koji Suematsu
  6. Takeda Pharmaceutical Company Limited, Osaka, Japan

    • Kenkichi Sugiura
    •  & Shyh-Yuh Liou
  7. Mitsubishi Tanabe Pharma Corporation, Osaka, Japan

    • Tomoko Kubota
    • , Shinji Miyoshi
    • , Kinya Okada
    •  & Naohisa Tsutsui

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  1. the Japan PGx Data Science Consortium (JPDSC)

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Competing interests

Shigeo Kamitsuji, Kazuyuki Nakazono, Woosung Yang, Yuki Sugaya, and Naoyuki Kamatani are employed by StaGen, Tokyo, Japan.

Corresponding author

Correspondence to Koji Suematsu.

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DOI

https://doi.org/10.1038/jhg.2015.23

Supplementary Information accompanies the paper on Journal of Human Genetics website (http://www.nature.com/jhg)

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