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- Japanese Population Structure, Based on SNP Genotypes from 7...Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies
The American Journal of Human Genetics, Volume 83, Issue 4, 10 October 2008, Pages 445-456
Yumi Yamaguchi-Kabata, Kazuyuki Nakazono, Atsushi Takahashi, Susumu Saito, Naoya Hosono, Michiaki Kubo, Yusuke Nakamura and Naoyuki Kamatani
AbstractBecause 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 gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the 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.
Abstract | Full Text | PDF (1065 kb) - Response to Lee et al.Response to Lee et al.
The American Journal of Human Genetics, Volume 82, Issue 2, 8 February 2008, Pages 526-528
Michael P. Epstein, Andrew S. Allen and Glen A. Satten
Full Text | PDF (88 kb) - Comment on a Simple and Improved Correction for Population S...Comment on a Simple and Improved Correction for Population Stratification
The American Journal of Human Genetics, Volume 82, Issue 2, 8 February 2008, Pages 524-526
Seunggeun Lee, Patrick F. Sullivan, Fei Zou and Fred A. Wright
Full Text | PDF (83 kb) - …more
Copyright © 2007 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 80, Issue 5, 948-956, 1 May 2007
doi:10.1086/513477
Report
Measuring European Population Stratification with Microarray Genotype Data
Marc Bauchet
, 
, Brian McEvoyb, Laurel N. Pearson, Ellen E. Quillen, Tamara Sarkisianc, Kristine Hovhannesyanc, d, Ranjan Dekae, Daniel G. Bradleyb and Mark D. Shriver
a Department of Anthropology, Pennsylvania State University, University Park
b Smurfit Institute of Genetics, Trinity College, Dublin
c Center of Medical Genetics and Primary Health Care, Yerevan, Armenia
d Centre de Recherche Hôpital Sainte-Justine, Université de Montréal, Montréal
e and Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati
Address for correspondence and reprints: Dr. Marc Bauchet, Department of Anthropology, Carpenter Building 409, Pennsylvania State University, University Park, PA 16801.Abstract
A proper understanding of population genetic stratification—differences in individual ancestry within a population—is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ∼10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Étude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent’s ancestry.
