Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns
Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns
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DOI：
10.1089/cmb.2008.0065
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发表时间：
2008-11-01
影响因子：
1.7
通讯作者：
Bertranpetit, Jaume
中科院分区：
文献类型：
--
作者：
Parida, Laxmi;Mele, Marta;Bertranpetit, Jaume
传统上，非重组基因组，即mtDNA或Y染色体，已被用于系统地理学，特别是便于分析。在这种情况下，系统发育结构的拓扑结构是一个无环图，它通常是一个树，易于理解，并且在某种程度上易于推断。然而，对于大多数基因组来说，重组是一个不可否认的遗传事实。由于需要更完整的分析，我们解决了从现存序列集合中估计祖先重组图（ARG）的问题。我们利用在人类单倍型中观察到的一致性作为模式，并提出了一个模式网络模型来重建ARG。我们在模拟上测试了我们的模型，这些模拟非常接近观察到的单倍型，并观察到有希望的结果。
Traditionally nonrecombinant genome, i.e., mtDNA or Y chromosome, has been used for phylogeography, notably for ease of analysis. The topology of the phylogeny structure in this case is an acyclic graph, which is often a tree, is easy to comprehend and is somewhat easy to infer. However, recombination is an undeniable genetic fact for most part of the genome. Driven by the need for a more complete analysis, we address the problem of estimating the ancestral recombination graph (ARG) from a collection of extant sequences. We exploit the coherence that is observed in the human haplotypes as patterns and present a network model of patterns to reconstruct the ARG. We test our model on simulations that closely mimic the observed haplotypes and observe promising results.