Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

Masao Nagasaki, Jun Yasuda, Fumiki Katsuoka, Naoki Nariai, Kaname Kojima, Yosuke Kawai, Yumi Yamaguchi-Kabata, Junji Yokozawa, Inaho Danjoh, Sakae Saito, Yukuto Sato, Takahiro Mimori, Kaoru Tsuda, Rumiko Saito, Xiaoqing Pan, Satoshi Nishikawa, Shin Ito, Yoko Kuroki, Osamu Tanabe, Nobuo FuseShinichi Kuriyama, Hideyasu Kiyomoto, Atsushi Hozawa, Naoko Minegishi, James Douglas Engel, Kengo Kinoshita, Shigeo Kure, Nobuo Yaegashi, Masayuki Yamamoto, Akito Tsuboi, Fuji Nagami, Hiroshi Kawame, Hiroaki Tomita, Ichiro Tsuji, Jun Nakaya, Junichi Sugawara, Kichiya Suzuki, Masahiro Kikuya, Michiaki Abe, Naoki Nakaya, Noriko Osumi, Riu Yamashita, Soichi Ogishima, Takako Takai, Teiji Tominaga, Yasuyuki Taki, Yoichi Suzuki

Research output: Contribution to journalArticle

174 Citations (Scopus)

Abstract

The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.

Original languageEnglish
Article number8018
JournalNature communications
Volume6
DOIs
Publication statusPublished - 2015 Aug 21

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Nagasaki, M., Yasuda, J., Katsuoka, F., Nariai, N., Kojima, K., Kawai, Y., Yamaguchi-Kabata, Y., Yokozawa, J., Danjoh, I., Saito, S., Sato, Y., Mimori, T., Tsuda, K., Saito, R., Pan, X., Nishikawa, S., Ito, S., Kuroki, Y., Tanabe, O., ... Suzuki, Y. (2015). Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nature communications, 6, [8018]. https://doi.org/10.1038/ncomms9018