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Human genetic variation database, a reference database of genetic variations in the Japanese population. 2016
Koichiro Higasa, and
Noriko Miyake, and
Jun Yoshimura, and
Kohji Okamura, and
Tetsuya Niihori, and
Hirotomo Saitsu, and
Koichiro Doi, and
Masakazu Shimizu, and
Kazuhiko Nakabayashi, and
Yoko Aoki, and
Yoshinori Tsurusaki, and
Shinichi Morishita, and
Takahisa Kawaguchi, and
Osuke Migita, and
Keiko Nakayama, and
Mitsuko Nakashima, and
Jun Mitsui, and
Maiko Narahara, and
Keiko Hayashi, and
Ryo Funayama, and
Daisuke Yamaguchi, and
Hiroyuki Ishiura, and
Wen-Ya Ko, and
Kenichiro Hata, and
Takeshi Nagashima, and
Ryo Yamada, and
Yoichi Matsubara, and
Akihiro Umezawa, and
Shoji Tsuji, and
Naomichi Matsumoto, and
Fumihiko Matsuda
Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/.
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October 2015,
Nature,
