Multiway Admixture Deconvolution Using Phased or Unphased Ancestral Panels
Multiway Admixture Deconvolution Using Phased or Unphased Ancestral Panels
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DOI：
10.1002/gepi.21692
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发表时间：
2013-01-01
影响因子：
2.1
通讯作者：
Marchini, Jonathan
中科院分区：
文献类型：
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作者：
Churchhouse, Claire;Marchini, Jonathan
我们描述了一种新的方法来推断地方血统的混合个人从密集的全基因组单核苷酸多态性数据。该方法，称为MULTIMIX，允许多个源人口，模型标记之间的人口连锁不平衡，并适用于数据集，其中的样本和源人口是定相或非定相。该模型是基于一个隐藏的马尔可夫模型的开关在连续窗口的基因座之间的祖先。我们使用多变量正态分布和从祖先面板估计的参数对每个窗口内观察到的单倍型进行建模。我们提出了三种方法来拟合模型马尔可夫链蒙特卡罗抽样，期望最大化算法，分类期望最大化算法。我们的方法在模拟与欧洲和西非血统混合的个体上的性能显示它与HAPMIX相当，两种方法的血统调用在三个参数组中的99.26%的位点上一致。除了它比HAPMIX更快之外，还发现它在涉及三个祖先种群的模拟中在混合物的范围内表现良好。在对真实的数据的分析中，我们估计了欧洲、西非和美洲土著血统对墨西哥HapMap样本中每个位点的贡献，给出了与先前报道一致的祖先比例的估计。
We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the modelMarkov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci across the three parameter groups. In addition to it being faster than HAPMIX, it is also found to perform well over a range of extent of admixture in a simulation involving three ancestral populations. In an analysis of real data, we estimate the contribution of European, West African and Native American ancestry to each locus in the Mexican samples of HapMap, giving estimates of ancestral proportions that are consistent with those previously reported.