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 - 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.
UR - http://www.scopus.com/inward/record.url?scp=85045995981&partnerID=8YFLogxK
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 -