title: Japan PGx Data Science Consortium Database: SNPs and HLA genotype data from 2994 Japanese healthy individuals for pharmacogenomics studies.
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.
authors: StaGen, Tokyo, Japan.
authors: Shigeo
authors: S
authors: Kamitsuji
authors: Astellas Pharma, Tokyo, Japan.
authors: Takashi
authors: T
authors: Matsuda
authors: Astellas Pharma, Tokyo, Japan.
authors: Koichi
authors: K
authors: Nishimura
authors: Daiichi Sankyo, Tokyo, Japan.
authors: Seiko
authors: S
authors: Endo
authors: Daiichi Sankyo, Tokyo, Japan.
authors: Chisa
authors: C
authors: Wada
authors: Daiichi Sankyo, Tokyo, Japan.
authors: Kenji
authors: K
authors: Watanabe
authors: Otsuka Pharmaceutical, Tokyo, Japan.
authors: Koichi
authors: K
authors: Hasegawa
authors: Otsuka Pharmaceutical, Tokyo, Japan.
authors: Haretsugu
authors: H
authors: Hishigaki
authors: Otsuka Pharmaceutical, Tokyo, Japan.
authors: Masatoshi
authors: M
authors: Masuda
authors: Taisho Pharmaceutical, Tokyo, Japan.
authors: Yusuke
authors: Y
authors: Kuwahara
authors: Taisho Pharmaceutical, Tokyo, Japan.
authors: Katsuki
authors: K
authors: Tsuritani
authors: Takeda Pharmaceutical Company Limited, Osaka, Japan.
authors: Kenkichi
authors: K
authors: Sugiura
authors: Mitsubishi Tanabe Pharma Corporation, Osaka, Japan.
authors: Tomoko
authors: T
authors: Kubota
authors: Mitsubishi Tanabe Pharma Corporation, Osaka, Japan.
authors: Shinji
authors: S
authors: Miyoshi
authors: Mitsubishi Tanabe Pharma Corporation, Osaka, Japan.
authors: Kinya
authors: K
authors: Okada
authors: StaGen, Tokyo, Japan.
authors: Kazuyuki
authors: K
authors: Nakazono
authors: StaGen, Tokyo, Japan.
authors: Yuki
authors: Y
authors: Sugaya
authors: StaGen, Tokyo, Japan.
authors: Woosung
authors: W
authors: Yang
authors: Astellas Pharma, Tokyo, Japan.
authors: Taiji
authors: T
authors: Sawamoto
authors: Astellas Pharma, Tokyo, Japan.
authors: Wataru
authors: W
authors: Uchida
authors: Daiichi Sankyo, Tokyo, Japan.
authors: Akira
authors: A
authors: Shinagawa
authors: Otsuka Pharmaceutical, Tokyo, Japan.
authors: Tsutomu
authors: T
authors: Fujiwara
authors: Taisho Pharmaceutical, Tokyo, Japan.
authors: Hisaharu
authors: H
authors: Yamada
authors: Taisho Pharmaceutical, Tokyo, Japan.
authors: Koji
authors: K
authors: Suematsu
authors: Mitsubishi Tanabe Pharma Corporation, Osaka, Japan.
authors: Naohisa
authors: N
authors: Tsutsui
authors: StaGen, Tokyo, Japan.
authors: Naoyuki
authors: N
authors: Kamatani
authors: Takeda Pharmaceutical Company Limited, Osaka, Japan.
authors: Shyh-Yuh
authors: SY
authors: Liou
mesh_terms: D030541:Databases, Genetic; D005260:Female; D005787:Gene Frequency; D056726:Genetic Association Studies; D005838:Genotype; D006680:HLA Antigens / Q000235:genetics*; D064368:Healthy Volunteers; D006801:Humans; D007564:Japan; D008297:Male; D010597:Pharmacogenetics; D020641:Polymorphism, Single Nucleotide
chemical_list: D006680:HLA Antigens