基因关联研究中的群体分层
Population Stratification in Genetic Association Studies.
作者信息
Hellwege Jacklyn N, Keaton Jacob M, Giri Ayush, Gao Xiaoyi, Velez Edwards Digna R, Edwards Todd L
机构信息
Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, Illinois.
出版信息
Curr Protoc Hum Genet. 2017 Oct 18;95:1.22.1-1.22.23. doi: 10.1002/cphg.48.
Abstract
Population stratification (PS) is a primary consideration in studies of genetic determinants of human traits. Failure to control for PS may lead to confounding, causing a study to fail for lack of significant results, or resources to be wasted following false-positive signals. Here, historical and current approaches for addressing PS when performing genetic association studies in human populations are reviewed. Methods for detecting the presence of PS, including global and local ancestry methods, are described. Also described are approaches for accounting for PS when calculating association statistics, such that measures of association are not confounded. Many traits are being examined for the first time in minority populations, which may inherently feature PS. © 2017 by John Wiley & Sons, Inc.
摘要
群体分层（PS）是人类性状遗传决定因素研究中的首要考虑因素。未能控制群体分层可能会导致混杂，致使研究因缺乏显著结果而失败，或者在出现假阳性信号后造成资源浪费。本文综述了在人类群体中进行基因关联研究时处理群体分层的历史方法和当前方法。描述了检测群体分层存在的方法，包括全局和局部祖先方法。还介绍了在计算关联统计量时考虑群体分层的方法，以使关联度量不被混淆。许多性状首次在少数群体中进行研究，而这些群体可能本身就存在群体分层特征。© 2017 约翰威立父子公司版权所有
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2
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3
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