The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection
The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection
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DOI：
10.1093/molbev/msh266
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发表时间：
2005-01-01
影响因子：
10.7
通讯作者：
Shen, Y
中科院分区：
文献类型：
--
作者：
Ding, KY;Zhou, K;Shen, Y
最近有人提出，人类基因组是由一系列单倍型模块组成的，创建全基因组单倍型图谱的工作已经在进行中。已经提出了几种计算算法来划分基因组。然而，对于它们在单倍型模块划分和单倍型标签单核苷酸多态性（SNP）选择方面的行为知之甚少。在此，我们对三类单倍型模块划分定义进行了系统比较，即基于多样性的方法、基于连锁不平衡（LD）的方法和基于重组的方法。所使用的数据来自于在均匀重组模型和假定重组热点的模型下的溯祖模拟。当在不同的群体遗传学情景下比较划分方法时，在熵的度量中，单倍型信息损失存在相当大的差异。在两种重组模型下，基于LD的定义和基于重组的定义的结果彼此之间比基于多样性的定义的结果更为相似。这项工作表明，在进行基于单倍型的关联作图时，单倍型模块定义和SNP选择需要仔细考虑。
It has been recently suggested that the human genome is organized as a series of haplotype blocks, and efforts to create a genome-wide haplotype map are already underway. Several computational algorithms have been proposed to partition the genome. However, little is known about their behaviors in relation to the haplotype-block partitioning and haplotype-tagging SNPs selection. Here, we present a systematic comparison of three classes of haplotype-block partition definitions, a diversity-based method, a linkage-disequilibrium (LD)-based method, and a recombination-based method. The data used were derived from a coalescent simulation under both a uniform recombination model and one that assumes recombination hotspots. There were considerable differences in haplotype information loss in the measure of entropy when the partition methods were compared under different population-genetics scenarios. Under both recombination models, the results from the LD-based definition and the recombination-based definition were more similar to each other than were the results from the diversity-based definition. This work demonstrates that when undertaking haplotype-based association mapping, the choice of haplotype-block definition and SNP selection requires careful consideration.