Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes

Yumi Yamaguchi-Kabata, Tatsuhiko Tsunoda, Natsuhiko Kumasaka, Atsushi Takahashi, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

研究成果: Article

6 引用 (Scopus)

抄録

Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388 591 autosomal SNPs from 18 379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.

元の言語English
ページ(範囲)326-334
ページ数9
ジャーナルJournal of Human Genetics
57
発行部数5
DOI
出版物ステータスPublished - 01-05-2012

Fingerprint

Haplotypes
Single Nucleotide Polymorphism
Genotype
Genome
Chromosomes, Human, Pair 4
Chromosomes, Human, Pair 6
Chromosomes, Human, Pair 3
Homozygote
HLA Antigens
Principal Component Analysis
Cell Adhesion
Population
Genes
Immune System

All Science Journal Classification (ASJC) codes

  • Genetics(clinical)
  • Genetics

これを引用

Yamaguchi-Kabata, Y., Tsunoda, T., Kumasaka, N., Takahashi, A., Hosono, N., Kubo, M., ... Kamatani, N. (2012). Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes. Journal of Human Genetics, 57(5), 326-334. https://doi.org/10.1038/jhg.2012.26
Yamaguchi-Kabata, Yumi ; Tsunoda, Tatsuhiko ; Kumasaka, Natsuhiko ; Takahashi, Atsushi ; Hosono, Naoya ; Kubo, Michiaki ; Nakamura, Yusuke ; Kamatani, Naoyuki. / Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes. :: Journal of Human Genetics. 2012 ; 巻 57, 番号 5. pp. 326-334.
@article{798c93a895214d2e88a2dbf249db0298,
title = "Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes",
abstract = "Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388 591 autosomal SNPs from 18 379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.",
author = "Yumi Yamaguchi-Kabata and Tatsuhiko Tsunoda and Natsuhiko Kumasaka and Atsushi Takahashi and Naoya Hosono and Michiaki Kubo and Yusuke Nakamura and Naoyuki Kamatani",
year = "2012",
month = "5",
day = "1",
doi = "10.1038/jhg.2012.26",
language = "English",
volume = "57",
pages = "326--334",
journal = "Journal of Human Genetics",
issn = "1434-5161",
publisher = "Nature Publishing Group",
number = "5",

}

Yamaguchi-Kabata, Y, Tsunoda, T, Kumasaka, N, Takahashi, A, Hosono, N, Kubo, M, Nakamura, Y & Kamatani, N 2012, 'Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes', Journal of Human Genetics, 巻. 57, 番号 5, pp. 326-334. https://doi.org/10.1038/jhg.2012.26

Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes. / Yamaguchi-Kabata, Yumi; Tsunoda, Tatsuhiko; Kumasaka, Natsuhiko; Takahashi, Atsushi; Hosono, Naoya; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki.

:: Journal of Human Genetics, 巻 57, 番号 5, 01.05.2012, p. 326-334.

研究成果: Article

TY - JOUR

T1 - Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes

AU - Yamaguchi-Kabata, Yumi

AU - Tsunoda, Tatsuhiko

AU - Kumasaka, Natsuhiko

AU - Takahashi, Atsushi

AU - Hosono, Naoya

AU - Kubo, Michiaki

AU - Nakamura, Yusuke

AU - Kamatani, Naoyuki

PY - 2012/5/1

Y1 - 2012/5/1

N2 - Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388 591 autosomal SNPs from 18 379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.

AB - Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388 591 autosomal SNPs from 18 379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.

UR - http://www.scopus.com/inward/record.url?scp=84861633465&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84861633465&partnerID=8YFLogxK

U2 - 10.1038/jhg.2012.26

DO - 10.1038/jhg.2012.26

M3 - Article

VL - 57

SP - 326

EP - 334

JO - Journal of Human Genetics

JF - Journal of Human Genetics

SN - 1434-5161

IS - 5

ER -