TY - JOUR
T1 - Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese
AU - Okada, Yukinori
AU - Momozawa, Yukihide
AU - Sakaue, Saori
AU - Kanai, Masahiro
AU - Ishigaki, Kazuyoshi
AU - Akiyama, Masato
AU - Kishikawa, Toshihiro
AU - Arai, Yasumichi
AU - Sasaki, Takashi
AU - Kosaki, Kenjiro
AU - Suematsu, Makoto
AU - Matsuda, Koichi
AU - Yamamoto, Kazuhiko
AU - Kubo, Michiaki
AU - Hirose, Nobuyoshi
AU - Kamatani, Yoichiro
N1 - Funding Information:
We thank Victor Renault for his helpful advices in constructing the WGS pipeline. We also thank Towfique Raj for his kind suggestions on natural selection analysis. This research was supported by the Tailor-Made Medical Treatment program (the BioBank Japan Project) of the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) and the Japan Agency for Medical Research and Development (AMED: 15km0305019h0101), and a grant from the Ministry of Health, Welfare, and Labor for the Scientific Research Project for Longevity (NH: 1999-2003). M.S. was supported by the BioBank Japan Project and the budget from Ministry of Agriculture until March, 2015. Y.O. was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (15H05670, 15H05907, 15H05911, 15K14429, 16H03269, and 16K15738), AMED (16km0405206h0001, 16gm6010001h0001, and 17ek0410041h0001), Takeda Science Foundation, the Uehara Memorial Foundation, the Naito Foundation, Daiichi Sankyo Foundation of Life Science, and Senri Life Science Foundation.
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-018-03274-0
DO - 10.1038/s41467-018-03274-0
M3 - Article
C2 - 29691385
AN - SCOPUS:85045995981
SN - 2041-1723
VL - 9
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 1631
ER -
