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 and Yoichiro Kamatani
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Yukinori Okada: Osaka University Graduate School of Medicine
Yukihide Momozawa: Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences
Saori Sakaue: Osaka University Graduate School of Medicine
Masahiro Kanai: Osaka University Graduate School of Medicine
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
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

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-03274-0

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