MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome
MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome
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DOI：
10.1177/1177932219873884
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发表时间：
2019-09-06
影响因子：
5.8
通讯作者：
Ueda, Shintaroh
中科院分区：
文献类型：
--
作者：
Ishiya, Koji;Mizuno, Fuzuki;Ueda, Shintaroh
部分人类线粒体基因组序列的不完整使得在多个资源之间进行相关比较变得困难。为了解决这个问题，我们提出了一个计算框架来推断人类线粒体基因组中缺失的核苷酸。我们将其应用于世界范围内的线粒体单倍群谱系并评估其性能。我们的方法可以在大多数人类线粒体DNA谱系中以0.99或更高的精度推断缺失的核苷酸。此外，尽管低覆盖率的线粒体基因组序列在多维尺度分析中往往导致关系模糊，但我们的方法可以根据相应的线粒体DNA谱系纠正这种位置排列。因此，我们的框架将提供一个实用的解决方案，以弥补在部分和碎片化的人类线粒体基因组序列中缺乏基因组覆盖。在这项研究中，我们开发了一个开源的计算机程序，MitoIMP，实现我们的imputation程序。MitoIMP可以从https://github.com/omicstools/mitoimp免费获得。
The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omicstools/mitoimp.