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

Yukinori Okada, Yukihide Momozawa, Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Masato Akiyama, Toshihiro Kishikawa, Yasumichi Arai, Takashi Sasaki, Kenjiro Kosaki, Makoto Suematsu, Koichi Matsuda, Kazuhiko Yamamoto, Michiaki Kubo, Nobuyoshi Hirose, Yoichiro Kamatani

研究成果: Article

30 引用 (Scopus)

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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.

元の言語English
記事番号1631
ジャーナルNature communications
9
発行部数1
DOI
出版物ステータスPublished - 2018 12 1

ASJC Scopus subject areas

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

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    Okada, Y., Momozawa, Y., Sakaue, S., Kanai, M., Ishigaki, K., Akiyama, M., Kishikawa, T., Arai, Y., Sasaki, T., Kosaki, K., Suematsu, M., Matsuda, K., Yamamoto, K., Kubo, M., Hirose, N., & Kamatani, Y. (2018). Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese. Nature communications, 9(1), [1631]. https://doi.org/10.1038/s41467-018-03274-0