Constructing founder sets under allelic and non-allelic homologous recombination.
Constructing founder sets under allelic and non-allelic homologous recombination.
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DOI：
10.1186/s13015-023-00241-3
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发表时间：
2023-09-29
影响因子：
1
通讯作者：
Doerr, Daniel
中科院分区：
文献类型：
--
作者：
Bonnet, Konstantinn;Marschall, Tobias;Doerr, Daniel
染色体的母本和父本之间的同源重组是人类遗传的关键机制，并塑造了我们物种的群体遗传特性。然而，类似的机制也可以在同一序列的不同拷贝之间起作用，然后被称为非等位基因同源重组(Nahr)。这一过程可能导致基因组重排--包括缺失、复制和倒位--并且是许多基因组疾病的基础。尽管它对基因组进化和疾病很重要，但缺乏计算模型来研究易患NaHR的基因组基因座。在这项工作中，我们提出了这样一个计算模型，为(等位)同源重组和NaHR提供了一个统一的框架。我们的模型将一组基因组表示为一张图，其中单倍型对应于浏览这张图。在我们的重组模型下，我们描述了两个方正问题，给出了求解它们的基于流的算法，描述了精确描述重组次数的方法，并展示了对实际问题实例的可伸缩性。网上版载有补充材料，可在10.1186/s13015-023-00241-3查阅。
Homologous recombination between the maternal and paternal copies of a chromosome is a key mechanism for human inheritance and shapes population genetic properties of our species. However, a similar mechanism can also act between different copies of the same sequence, then called non-allelic homologous recombination (NAHR). This process can result in genomic rearrangements—including deletion, duplication, and inversion—and is underlying many genomic disorders. Despite its importance for genome evolution and disease, there is a lack of computational models to study genomic loci prone to NAHR. In this work, we propose such a computational model, providing a unified framework for both (allelic) homologous recombination and NAHR. Our model represents a set of genomes as a graph, where haplotypes correspond to walks through this graph. We formulate two founder set problems under our recombination model, provide flow-based algorithms for their solution, describe exact methods to characterize the number of recombinations, and demonstrate scalability to problem instances arising in practice. The online version contains supplementary material available at 10.1186/s13015-023-00241-3.
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