Bercovici Sivan, Geiger Dan
Computer Science Department , Technion, Haifa, Israel .
J Comput Biol. 2009 Aug;16(8):1141-50. doi: 10.1089/cmb.2009.0105.
Much effort has recently been invested in developing methods for determining the ancestral origin of chromosomal segments in admixed individuals. Motivations for this task are the study of population history such as bottleneck effects and migration, the assessment of population stratification for adequate adjustment of association studies, and the enhancement of mapping by admixture linkage disequilibrium (MALD). In this article, we present a novel framework for the inference of ancestry at each chromosomal location. The uniqueness of our method stems from the ability to incorporate complex probability models that account for linkage-disequilibrium in the ancestral populations. We provide an inference algorithm that is polynomial in the number of markers even though the underlying problem seems to be inherently exponential in nature. We demonstrate the validity of our model and conclude that, with sufficient ancestral haplotypes, this framework can provide higher accuracy in inferring ancestral origin.
最近，人们投入了大量精力来开发确定混合个体中染色体片段祖先起源的方法。开展这项工作的动机包括对群体历史（如瓶颈效应和迁移）的研究、对群体分层进行评估以适当调整关联研究，以及通过混合连锁不平衡（MALD）增强定位。在本文中，我们提出了一个用于推断每个染色体位置祖先的新框架。我们方法的独特之处在于能够纳入复杂的概率模型，这些模型考虑了祖先群体中的连锁不平衡。我们提供了一种推理算法，该算法在标记数量上是多项式的，尽管潜在问题本质上似乎是指数级的。我们证明了我们模型的有效性，并得出结论，在有足够的祖先单倍型的情况下，这个框架可以在推断祖先起源方面提供更高的准确性。
