Xing Jinchuan, Witherspoon David J, Watkins W Scott, Zhang Yuhua, Tolpinrud Whitney, Jorde Lynn B
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
Genomics. 2008 Jul;92(1):41-51. doi: 10.1016/j.ygeno.2008.03.011. Epub 2008 May 14.
Linkage disequilibrium (LD) has received much attention recently because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian sample and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r(2) >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations.
连锁不平衡（LD）因其在定位致病基因方面的价值，近年来备受关注。由于人类基因组中相邻基因座之间存在广泛的连锁不平衡，人们认为可以选择一个区域内的单核苷酸多态性子集（标签单核苷酸多态性，tagSNPs）来捕获大多数其余的单核苷酸多态性变体。在本研究中，我们检测了300多名个体的连锁不平衡模式和HapMap标签单核苷酸多态性的可转移性。纳入了一个南印度样本和一个非洲姆布蒂俾格米人群样本，以评估HapMap标签单核苷酸多态性在地理上不同且基因隔离人群中的性能。我们的结果表明，r(2) >= 0.8选择的HapMap标签单核苷酸多态性能够捕获来自同一大陆组人群中85%以上的单核苷酸多态性。来自HapMap CEU和CHB+JPT的组合标签单核苷酸多态性是印度样本的最佳参考。HapMap YRI是俾格米人样本中标签单核苷酸多态性选择的充分参考。除了我们的研究结果，我们还回顾了25项以上关于标签单核苷酸多态性可转移性的近期研究，并提出了从HapMap的人群中选择标签单核苷酸多态性的一般指南。
