Multiple haplotype reconstruction from allele frequency data
Multiple haplotype reconstruction from allele frequency data
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DOI：
10.1038/s43588-021-00056-5
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发表时间：
2021-04-01
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影响因子：
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通讯作者：
Futschik, Andreas
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文献类型：
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作者：
Pelizzola, Marta;Behr, Merle;Futschik, Andreas
由于单倍型信息在生物医学应用中具有广泛的意义，人们一直在努力重建单倍型。在这里，我们提出了一种有效的方法，称为haploSep，它能够准确地推断主要单倍型和它们的频率，只是从多个样本的等位基因频率数据。甚至实验获得的等位基因频率的准确性可以通过从我们重建的单倍型重新估计它们来提高。从方法论的角度来看，我们的问题作为一个多元回归问题，设计矩阵和系数矩阵都是未知的。与其他方法相比，haploSep非常快速，计算复杂度与单体型长度成线性关系。我们说明了我们的方法模拟和真实的数据集中在实验进化和微生物数据。
Because haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose an efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes. From a methodological point of view, we model our problem as a multivariate regression problem where both the design matrix and the coefficient matrix are unknown. Compared to other methods, haploSep is very fast, with linear computational complexity in the haplotype length. We illustrate our method on simulated and real data focusing on experimental evolution and microbial data.