Common deletions and SNPs are in linkage disequilibrium in the human genome
Common deletions and SNPs are in linkage disequilibrium in the human genome
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DOI：
10.1038/ng1695
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发表时间：
2006-01-01
期刊：
影响因子：
30.8
通讯作者：
Frazer, KA
中科院分区：
文献类型：
--
作者：
Hinds, DA;Kloek, AP;Frazer, KA
人类在诸如身高、眼睛颜色和对疾病的易感性等表型特征上表现出很大的差异。个体之间的基因组DNA序列差异是造成这些复杂性状遗传成分的原因。报告表明，中等和大规模的DNA拷贝数和结构变异普遍存在，足以成为个体之间遗传变异的重要来源（1-8）。由于鉴定与特定表型性状相关的基因组位点的关联研究主要集中在基因分型snp上，因此确定常见结构多态性是否与常见snp存在连锁不平衡是很重要的，因此可以在基于snp的研究中间接评估。在这里，我们研究了100个缺失多态性，范围从70 bp到7 kb。我们发现，用相似标准确定的共同缺失和snp与周围snp的连锁不平衡分布基本相同，这表明这些多态性可能具有共同的进化史，并且在基于snp的关联研究中，大多数缺失多态性可以通过代理有效地分析。
Humans show great variation in phenotypic traits such as height, eye color and susceptibility to disease. Genomic DNA sequence differences among individuals are responsible for the inherited components of these complex traits. Reports suggest that intermediate and large-scale DNA copy number and structural variations are prevalent enough to be an important source of genetic variation between individuals(1-8). Because association studies to identify genomic loci associated with particular phenotypic traits have focused primarily on genotyping SNPs, it is important to determine whether common structural polymorphisms are in linkage disequilibrium with common SNPs, and thus can be assessed indirectly in SNP-based studies. Here we examine 100 deletion polymorphisms ranging from 70 bp to 7 kb. We show that common deletions and SNPs ascertained with similar criteria have essentially the same distribution of linkage disequilibrium with surrounding SNPs, indicating that these polymorphisms may share evolutionary history and that most deletion polymorphisms are effectively assayed by proxy in SNP-based association studies.