Resolving complex structural genomic rearrangements using a randomized approach.
Resolving complex structural genomic rearrangements using a randomized approach.
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DOI：
10.1186/s13059-016-0993-1
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发表时间：
2016-06-10
期刊：
影响因子：
12.3
通讯作者：
Mills RE
中科院分区：
文献类型：
--
作者：
Zhao X;Emery SB;Myers B;Kidd JM;Mills RE
复杂染色体重排是结构性基因组改变，涉及缺失、重复、倒位或易位的多个实例，其共同发生在同一染色体上或代表同源染色体上的不同重叠事件。我们提出了SVelter，一种算法，该算法识别基因组的区域怀疑窝藏一个复杂的事件，然后通过迭代重排本地基因组结构，以随机的方式解决结构，每个结构对观察到的测序数据的特征进行评分。与已经用短读段和长读段深度测序的充分表征的基因组相比，SVelter能够准确地重建复杂的染色体重排。本文的在线版本（doi：10.1186/s13059-016-0993-1）包含补充材料，可供授权用户使用。
Complex chromosomal rearrangements are structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome or represent different overlapping events on homologous chromosomes. We present SVelter, an algorithm that identifies regions of the genome suspected to harbor a complex event and then resolves the structure by iteratively rearranging the local genome structure, in a randomized fashion, with each structure scored against characteristics of the observed sequencing data. SVelter is able to accurately reconstruct complex chromosomal rearrangements when compared to well-characterized genomes that have been deeply sequenced with both short and long reads. The online version of this article (doi:10.1186/s13059-016-0993-1) contains supplementary material, which is available to authorized users.