Genorne-wide SNP typing reveals signatures of population history
Genorne-wide SNP typing reveals signatures of population history
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DOI：
10.1016/j.ygeno.2008.03.005
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发表时间：
2008-07-01
期刊：
影响因子：
4.4
通讯作者：
Yeager, Meredith
中科院分区：
文献类型：
--
作者：
Hughes, Austin L.;Welch, Robert;Yeager, Meredith
单核苷酸多态性（SNP）阵列已成为一种流行的技术，用于疾病相关性研究，但他们也有潜力研究人类群体的遗传分化。将Affyssin基因芯片人类图谱500 K阵列集应用于代表美国主要种族群体（非洲人，亚洲人，欧洲人和西班牙人）的102个个体的人群，揭示了反映人口历史的基因多样性和遗传距离的模式。我们分析了388，654个常染色体SNP位点的等位基因频率，这些位点在我们的研究人群中显示出一些变异，缺失值为10%或更少。尽管每个亚群的规模较小（23-31个个体），但任何两个亚群之间在任何地点都没有固定的差异。正如现代人的非洲起源所预期的那样，非洲人的基因多样性比亚洲人或欧洲人都要大，亚洲人和欧洲人之间的遗传距离明显低于这两个人群中的任何一个与非洲人之间的遗传距离。应用于个体间相关矩阵的主成分分析能够完全分离出人类的主要大陆群体（非洲人，亚洲人和欧洲人），而西班牙裔则与所有这三个群体重叠。含有两个或两个以上的标记，亚群之间的遗传距离非常高的基因被确定为亚群之间的健康差异的候选基因。研究结果表明，即使样本量不大，全基因组SNP基因分型技术在捕获人类亚群之间基因频率差异的特征方面也有很大的潜力，可应用于法医学和种族健康差异研究等领域。(C)2008年爱思唯尔公司All rights reserved.
Single-nucleotide polymorphism (SNP) arrays have become a popular technology for disease-association studies, but they also have potential for studying the genetic differentiation of human populations. Application of the Affymetrix GeneChip Human Mapping 500K Array Set to a population of 102 individuals representing the major ethnic groups in the United States (African, Asian, European, and Hispanic) revealed patterns of gene diversity and genetic distance that reflected population history. We analyzed allelic frequencies at 388,654 autosomal SNP sites that showed some variation in our study population and 10% or fewer missing values. Despite the small size (23-31 individuals) of each subpopulation, there were no fixed differences at any site between any two subpopulations. As expected from the African origin of modern humans, greater gene diversity was seen in Africans than in either Asians or Europeans, and the genetic distance between the Asian and the European populations was significantly lower than that between either of these two populations and Africans. Principal components analysis applied to a correlation matrix among individuals was able to separate completely the major continental groups of humans (Africans, Asians, and Europeans), while Hispanics overlapped all three of these groups. Genes containing two or more markers with extraordinarily high genetic distance between subpopulations were identified as candidate genes for health differences between subpopulations. The results show that, even with modest sample sizes, genome-wide SNP genotyping technologies have great promise for capturing signatures of gene frequency difference between human subpopulations, with applications in areas as diverse as forensics and the study of ethnic health disparities. (C) 2008 Elsevier Inc. All rights reserved.