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Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Author

Listed:
  • Yukinori Okada

    (Osaka University Graduate School of Medicine
    Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences
    Osaka University)

  • Yukihide Momozawa

    (Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences)

  • Saori Sakaue

    (Osaka University Graduate School of Medicine
    Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences
    Graduate School of Medicine, the University of Tokyo)

  • Masahiro Kanai

    (Osaka University Graduate School of Medicine
    Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences
    Harvard Medical School)

  • Kazuyoshi Ishigaki

    (Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences)

  • Masato Akiyama

    (Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences)

  • Toshihiro Kishikawa

    (Osaka University Graduate School of Medicine
    Osaka University Graduate School of Medicine)

  • Yasumichi Arai

    (Keio University School of Medicine)

  • Takashi Sasaki

    (Keio University School of Medicine)

  • Kenjiro Kosaki

    (Keio University School of Medicine)

  • Makoto Suematsu

    (Keio University School of Medicine)

  • Koichi Matsuda

    (The University of Tokyo)

  • Kazuhiko Yamamoto

    (Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences)

  • Michiaki Kubo

    (RIKEN Center for Integrative Medical Sciences)

  • Nobuyoshi Hirose

    (Keio University School of Medicine)

  • Yoichiro Kamatani

    (Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences
    Kyoto University Graduate School of Medicine)

Abstract

Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000–3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu). While the selection signatures do not show enrichment in archaic hominin-derived genome sequences, they overlap with the SNPs associated with the modern human traits. The strongest overlaps are observed for the alcohol or nutrition metabolism-related traits. Our study illustrates the value of high-depth WGS to understand evolution and their relationship with disease risk.

Suggested Citation

  • Yukinori Okada & Yukihide Momozawa & Saori Sakaue & Masahiro Kanai & Kazuyoshi Ishigaki & Masato Akiyama & Toshihiro Kishikawa & Yasumichi Arai & Takashi Sasaki & Kenjiro Kosaki & Makoto Suematsu & Ko, 2018. "Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03274-0
    DOI: 10.1038/s41467-018-03274-0
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    Cited by:

    1. Kenichi Yamamoto & Kyuto Sonehara & Shinichi Namba & Takahiro Konuma & Hironori Masuko & Satoru Miyawaki & Yoichiro Kamatani & Nobuyuki Hizawa & Keiichi Ozono & Loic Yengo & Yukinori Okada, 2023. "Genetic footprints of assortative mating in the Japanese population," Nature Human Behaviour, Nature, vol. 7(1), pages 65-73, January.
    2. Go Sato & Yuya Shirai & Shinichi Namba & Ryuya Edahiro & Kyuto Sonehara & Tsuyoshi Hata & Mamoru Uemura & Koichi Matsuda & Yuichiro Doki & Hidetoshi Eguchi & Yukinori Okada, 2023. "Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Kyuto Sonehara & Yui Kimura & Yoshiko Nakano & Tatsuya Ozawa & Meiko Takahashi & Ken Suzuki & Takashi Fujii & Yuko Matsushita & Arata Tomiyama & Toshihiro Kishikawa & Kenichi Yamamoto & Tatsuhiko Nait, 2022. "A common deletion at BAK1 reduces enhancer activity and confers risk of intracranial germ cell tumors," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    4. Pei-Kuan Cong & Wei-Yang Bai & Jin-Chen Li & Meng-Yuan Yang & Saber Khederzadeh & Si-Rui Gai & Nan Li & Yu-Heng Liu & Shi-Hui Yu & Wei-Wei Zhao & Jun-Quan Liu & Yi Sun & Xiao-Wei Zhu & Pian-Pian Zhao , 2022. "Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Kyuto Sonehara & Yoshitaka Yano & Tatsuhiko Naito & Shinobu Goto & Hiroyuki Yoshihara & Takahiro Otani & Fumiko Ozawa & Tamao Kitaori & Koichi Matsuda & Takashi Nishiyama & Yukinori Okada & Mayumi Sug, 2024. "Common and rare genetic variants predisposing females to unexplained recurrent pregnancy loss," Nature Communications, Nature, vol. 15(1), pages 1-9, December.

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