Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies
Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies
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DOI：
10.1016/j.ajhg.2008.08.019
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发表时间：
2008-10-10
影响因子：
9.8
通讯作者：
Kamatani, Naoyuki
中科院分区：
文献类型：
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作者：
Yamaguchi-Kabata, Yumi;Nakazono, Kazuyuki;Kamatani, Naoyuki
由于人群分层在病例对照研究中可能导致虚假的关联，因此了解人群结构非常重要。在这里，我们通过“特征分析”检查了日本的人口结构，在HapMap项目中使用了7003个日本人，以及60个欧洲人，60个非洲人和90个东亚人的140,387个snp的基因型。大多数日本人属于两个主要群体，本州和琉球；本岛群包括大部分来自日本主要岛屿的个体，琉球群包括大部分来自冲绳的个体。在6号染色体的HLA区域发现了本岛人和琉球人之间频率差异最大的snp。在红岛和琉球群体中，频率差异最大的非同义snp是EDAR基因的Val/Ala多态性（rs3827760），与毛发厚度相关；ABCC11基因的Gly/Ala多态性（rs17822931），与耳垢类型相关。在日本最大的岛屿本州岛，甚至在不同地区也观察到遗传分化。模拟研究表明，当样本量较大时，病例组和对照组中来自日本不同地区的不同比例的个体可能导致假阳性结果的膨胀率。
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.