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PMID: 29691385 Published · epublish English Journal Article Meta-Analysis Research Support, Non-U.S. Gov't

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

Nature communications ·Vol. 9 ·No. 1 ·2018-00-24 ·Pages 1631

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

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.

MeSH Terms
Aldehyde Dehydrogenase, Mitochondrial/genetics Animals Asians/genetics Disease/genetics Evolution, Molecular Gene Frequency Genome, Human Genome-Wide Association Study Hominidae/genetics Humans Japan Polymorphism, Single Nucleotide Quantitative Trait Loci Selection, Genetic Whole Genome Sequencing
Chemicals
ALDH2 protein, human Aldehyde Dehydrogenase, Mitochondrial
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Okada Yukinori ORCID
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan. [email protected]. | Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. [email protected]. | Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, 565-0871, Japan. [email protected].
Momozawa Yukihide
Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Sakaue Saori
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan. | Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. | Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-8655, Japan.
Kanai Masahiro ORCID
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan. | Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. | Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
Ishigaki Kazuyoshi
Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Akiyama Masato
Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Kishikawa Toshihiro
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan. | Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
Arai Yasumichi
Center for Supercentenarian Medical Research, Keio University School of Medicine, Shinanomachi 35, Shinjuku-ku, Tokyo, 160-8582, Japan.
Sasaki Takashi ORCID
Center for Supercentenarian Medical Research, Keio University School of Medicine, Shinanomachi 35, Shinjuku-ku, Tokyo, 160-8582, Japan.
Kosaki Kenjiro
Center for Medical Genetics, Keio University School of Medicine, Shinanomachi 35, Shinjuku-ku, Tokyo, 160-8582, Japan.
Suematsu Makoto
Department of Biochemistry, Keio University School of Medicine, Shinanomachi 35, Shinjuku-ku, Tokyo, 160-8582, Japan.
Matsuda Koichi
Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan.
Yamamoto Kazuhiko
Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Kubo Michiaki
RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Hirose Nobuyoshi
Center for Supercentenarian Medical Research, Keio University School of Medicine, Shinanomachi 35, Shinjuku-ku, Tokyo, 160-8582, Japan.
Kamatani Yoichiro ORCID
Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. | Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, 606-8507, Japan.
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Article Info
Journal
Nature communications
Abbr.
Nat Commun
ISSN
2041-1723
DOI
10.1038/s41467-018-03274-0
Email
[email protected]
Published
2018-00-24
Epub
2018-00-24
Pages
1631
Language
English
Region
England
NLM ID
101528555
PMCID
PMC5915442
Subset
IM
External Links
PubMed source DOI: 10.1038/s41467-018-03274-0 PMC Full Text View journal details
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