Dissecting linkage disequilibrium in African-American genomes: roles of markers and individuals.
Dissecting linkage disequilibrium in African-American genomes: roles of markers and individuals.
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DOI：
10.1093/molbev/msm135
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发表时间：
2007-09
影响因子：
10.7
通讯作者：
Shuhua Xu;Wei Huang;Haifeng Wang;Yungang He;Ying Wang;Yi Wang;J. Qian;M. Xiong;Li Jin
中科院分区：
文献类型：
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作者：
Shuhua Xu;Wei Huang;Haifeng Wang;Yungang He;Ying Wang;Yi Wang;J. Qian;M. Xiong;Li Jin
在最近的混合人群中，如非洲裔美国人（AfA），观察到连锁不平衡（LD）在幅度和范围上都有实质性的增加。另一方面，也有研究表明，非洲非洲人的LD与非洲人的LD非常相似。在这项研究中，我们试图通过对AfA个体样本进行24341个单核苷酸多态性（SNPs）的基因分型，对AfAs的LD结构进行系统检查，以解决这些矛盾的观察结果，这些SNP分布在几乎整个21号染色体上，平均密度为1.5 kb/SNP。非洲裔人口的总体死亡率与非洲人口相似，远低于欧洲人口。即使使用遗传信息标记（AIMs），也发现AfA的扩展LD仅限于一定的量级范围（0.2 < or = r(2) < or = 0.8）和一定的距离范围，即标记间距离大于200kb。此外，具有主要非洲血统的AfA个体被发现降低了LD的总体大小。与亲本群体相比，AfA群体的LD升高只能在有限的情况下，在两个亲本群体之间等位基因频率差异较大的标记上观察到。完全非洲血统的AfA个体对AfA人群的扩展LD贡献很小，仅使用混合个体进行进一步的基因分型或关联分析可能会提高统计能力，并可能降低成本。
Substantial increases of linkage disequilibrium (LD) both in magnitude and in range have been observed in recently admixed populations such as African-American (AfA). On the other hand, it has also been shown that LD in AfAs was very similar to that of African. In this study, we attempted to resolve these contradicting observations by conducting a systematic examination of the LD structure in AfAs by genotyping a sample of AfA individuals at 24,341 single nucleotide polymorphisms (SNPs) spanning almost the entire chromosome 21, with an average density of 1.5 kb/SNP. The overall LD in AfAs is similar to that in African populations and much less than that in European populations. Even when the ancestry-informative markers (AIMs) were used, extended LD in AfA was found to be limited to certain magnitude range (0.2 < or = r(2) < or = 0.8) and certain distance range, that is, between-marker distance more than 200 kb. Furthermore, the inclusion of AfA individuals with predominant African ancestry was found to reduce the overall magnitude of LD. Elevation of LD in the AfA population, compared with its parental populations, can only be observed at the markers with large allele frequency differences between 2 parental populations at limited scenario. AfA individuals of wholly African ancestry contribute little to the extended LD in the AfA population, and further genotyping or association analysis conducted using only admixed individuals may lead to higher statistical power and possibly reduced cost.