Inference of locus-specific ancestry in closely related populations.
Inference of locus-specific ancestry in closely related populations.
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DOI：
10.1093/bioinformatics/btp197
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发表时间：
2009-06-15
期刊：
影响因子：
--
通讯作者：
Halperin E
中科院分区：
文献类型：
--
作者：
Pasaniuc B;Sankararaman S;Kimmel G;Halperin E
最近混合种群的遗传变异的特征可以揭示历史种群事件，并有助于通过关联研究和混合作图来检测与疾病相关的单核苷酸多态(SNPs)。对特定基因座祖先的推断是我们理解这类群体遗传变异的关键。虽然当祖先群体(如非洲裔美国人)相距较远时，一些推断特定于座位的祖先的方法是准确的，但目前的方法在推断祖先群体密切相关的混合群体(例如，欧洲裔美国人)中的特定座位祖先时会导致很大的错误率。结果：在这项工作中，我们通过引入一个改进的重组事件模型，扩展了以前的基因座特异性祖先推断方法。我们提出了一种有效的动态规划算法来推断该模型中特定于座位的祖先，从而获得了一种提高精度的方法；当祖先群体关系密切时，这种改善是最显著的。对广泛的场景的评估，包括来自人类基因组多样性项目的52个种群的混合物，表明使用我们的方法确实可以在这些混合物中准确地推断出特定于座位的祖先。最后，我们证明，当应用于混合种群时，可以通过结合特定的基因座祖先来改进补偿方法。可获得性：WINPOP模型的实施作为LAMP包的一部分，可通过http://lamp.icsi.berkeley.edu/lamp联系：heran@icsi.berkeley.edu
A characterization of the genetic variation of recently admixed populations may reveal historical population events, and is useful for the detection of single nucleotide polymorphisms (SNPs) associated with diseases through association studies and admixture mapping. Inference of locus-specific ancestry is key to our understanding of the genetic variation of such populations. While a number of methods for the inference of locus-specific ancestry are accurate when the ancestral populations are quite distant (e.g. African–Americans), current methods incur a large error rate when inferring the locus-specific ancestry in admixed populations where the ancestral populations are closely related (e.g. Americans of European descent). Results: In this work, we extend previous methods for the inference of locus-specific ancestry by the incorporation of a refined model of recombination events. We present an efficient dynamic programming algorithm to infer the locus-specific ancestries in this model, resulting in a method that attains improved accuracies; the improvement is most significant when the ancestral populations are closely related. An evaluation on a wide range of scenarios, including admixtures of the 52 population groups from the Human Genome Diversity Project demonstrates that locus-specific ancestry can indeed be accurately inferred in these admixtures using our method. Finally, we demonstrate that imputation methods can be improved by the incorporation of locus-specific ancestry, when applied to admixed populations. Availability: The implementation of the WINPOP model is available as part of the LAMP package at http://lamp.icsi.berkeley.edu/lamp Contact: heran@icsi.berkeley.edu
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