Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies

Yumi Yamaguchi-Kabata, Kazuyuki Nakazono, Atsushi Takahashi, Susumu Saito, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura, Naoyuki Kamatani

Research output: Contribution to journalArticle

239 Citations (Scopus)

Abstract

Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by "Eigenanalysis," using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.

Original languageEnglish
Pages (from-to)445-456
Number of pages12
JournalAmerican Journal of Human Genetics
Volume83
Issue number4
DOIs
Publication statusPublished - 10-10-2008

Fingerprint

Ethnic Groups
Islands
Single Nucleotide Polymorphism
Japan
Genotype
Cerumen
HapMap Project
Population
Chromosomes, Human, Pair 6
Sample Size
Hair
Genes
Case-Control Studies
Control Groups

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Yamaguchi-Kabata, Yumi ; Nakazono, Kazuyuki ; Takahashi, Atsushi ; Saito, Susumu ; Hosono, Naoya ; Kubo, Michiaki ; Nakamura, Yusuke ; Kamatani, Naoyuki. / Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups : Effects on Population-Based Association Studies. In: American Journal of Human Genetics. 2008 ; Vol. 83, No. 4. pp. 445-456.
@article{17bee511a8284e6084b011ff8eac1fbc,
title = "Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies",
abstract = "Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by {"}Eigenanalysis,{"} using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.",
author = "Yumi Yamaguchi-Kabata and Kazuyuki Nakazono and Atsushi Takahashi and Susumu Saito and Naoya Hosono and Michiaki Kubo and Yusuke Nakamura and Naoyuki Kamatani",
year = "2008",
month = "10",
day = "10",
doi = "10.1016/j.ajhg.2008.08.019",
language = "English",
volume = "83",
pages = "445--456",
journal = "American Journal of Human Genetics",
issn = "0002-9297",
publisher = "Cell Press",
number = "4",

}

Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups : Effects on Population-Based Association Studies. / Yamaguchi-Kabata, Yumi; Nakazono, Kazuyuki; Takahashi, Atsushi; Saito, Susumu; Hosono, Naoya; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki.

In: American Journal of Human Genetics, Vol. 83, No. 4, 10.10.2008, p. 445-456.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups

T2 - Effects on Population-Based Association Studies

AU - Yamaguchi-Kabata, Yumi

AU - Nakazono, Kazuyuki

AU - Takahashi, Atsushi

AU - Saito, Susumu

AU - Hosono, Naoya

AU - Kubo, Michiaki

AU - Nakamura, Yusuke

AU - Kamatani, Naoyuki

PY - 2008/10/10

Y1 - 2008/10/10

N2 - Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by "Eigenanalysis," using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.

AB - Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by "Eigenanalysis," using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.

UR - http://www.scopus.com/inward/record.url?scp=53049090475&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=53049090475&partnerID=8YFLogxK

U2 - 10.1016/j.ajhg.2008.08.019

DO - 10.1016/j.ajhg.2008.08.019

M3 - Article

C2 - 18817904

AN - SCOPUS:53049090475

VL - 83

SP - 445

EP - 456

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 4

ER -