Identity-by-descent-based phasing and imputation in founder populations using graphical models
Identity-by-descent-based phasing and imputation in founder populations using graphical models
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DOI：
10.1002/gepi.20635
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发表时间：
2011-12-01
影响因子：
2.1
通讯作者：
Durbin, Richard
中科院分区：
文献类型：
--
作者：
Palin, Kimmo;Campbell, Harry;Durbin, Richard
单倍型的准确知识，等位基因的组合共同驻留在一个单一拷贝的染色体上，使强大的基因定位和序列插补方法。由于人类是二倍体，单倍型必须通过定相过程从基因型中获得。在这项研究中，我们提出了一个新的计算模型，单倍型定相的基础上成对共享的单倍型推断是相同的血统（IBD）。我们应用贝叶斯网络为基础的模型在一个新的定相算法，称为系统的远程定相（SLRP），可以利用在孤立的创始人群体的密切的遗传关系，并显示与模拟和真实的全基因组基因型数据，SLRP大大降低了定相错误率相比，以前的定相算法。此外，该方法准确地识别IBD的区域，使得能够进行无谱系的连锁研究，并且可以用于以非常低的错误率估算大多数基因型。Genet.流行病学2011. (C)2011 Wiley Periodicals，Inc.35：853-860，2011
Accurate knowledge of haplotypes, the combination of alleles co-residing on a single copy of a chromosome, enables powerful gene mapping and sequence imputation methods. Since humans are diploid, haplotypes must be derived from genotypes by a phasing process. In this study, we present a new computational model for haplotype phasing based on pairwise sharing of haplotypes inferred to be Identical-By-Descent (IBD). We apply the Bayesian network based model in a new phasing algorithm, called systematic long-range phasing (SLRP), that can capitalize on the close genetic relationships in isolated founder populations, and show with simulated and real genome-wide genotype data that SLRP substantially reduces the rate of phasing errors compared to previous phasing algorithms. Furthermore, the method accurately identifies regions of IBD, enabling linkage-like studies without pedigrees, and can be used to impute most genotypes with very low error rate. Genet. Epidemiol. 2011. (C) 2011 Wiley Periodicals, Inc.35:853-860, 2011