Haplotype reconstruction from genotype data using Imperfect Phylogeny
Haplotype reconstruction from genotype data using Imperfect Phylogeny
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DOI：
10.1093/bioinformatics/bth149
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发表时间：
2004-08-12
期刊：
影响因子：
5.8
通讯作者：
Eskin, E
中科院分区：
文献类型：
--
作者：
Halperin, E;Eskin, E
对复杂疾病的遗传基础的理解的关键是人类变异的建模。这种变异的大部分可以通过单核苷酸多态性（SNP）来表征，所述单核苷酸多态性是在单核苷酸位置处的突变。为了表征不同人之间的遗传变异，我们必须确定个体的单倍型或每条染色体上这些常见SNP的每个位置上出现的核苷酸碱基。在本文中，我们提出了一个高度准确的方法，从基因型数据的单倍型分辨率的结果。我们的方法利用了一个新的洞察的单倍型的基础结构，表明SNPs组织在高度相关的“块”。在最近的一些研究中，人类基因组的相当大的部分被划分为区块，使得大多数测序的基因型在每个区块中具有大约四种常见单倍型之一。我们的方法将SNPs划分为块，并且对于每个块，我们预测常见的单倍型和每个个体的单倍型。我们通过生物数据评估我们的方法。我们的方法预测常见的单倍型完美，并具有非常低的错误率（
Critical to the understanding of the genetic basis for complex diseases is the modeling of human variation. Most of this variation can be characterized by single nucleotide polymorphisms (SNPs) which are mutations at a single nucleotide position. To characterize the genetic variation between different people, we must determine an individual's haplotype or which nucleotide base occurs at each position of these common SNPs for each chromosome. In this paper, we present results for a highly accurate method for haplotype resolution from genotype data. Our method leverages a new insight into the underlying structure of haplotypes that shows that SNPs are organized in highly correlated 'blocks'. In a few recent studies, considerable parts of the human genome were partitioned into blocks, such that the majority of the sequenced genotypes have one of about four common haplotypes in each block. Our method partitions the SNPs into blocks, and for each block, we predict the common haplotypes and each individual's haplotype. We evaluate our method over biological data. Our method predicts the common haplotypes perfectly and has a very low error rate (