寻找与基因组结构变异相关的测序信号异常

IF 4.033 Q4 Biochemistry, Genetics and Molecular Biology
I. V. Bezdvornykh, N. A. Cherkasov, A. A. Kanapin, A. A. Samsonova
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引用次数: 0

摘要

摘要基因组结构变异(SV)是遗传多样性的主要来源之一。结构变异作为诱变剂可能会严重影响人类健康,导致遗传性疾病和癌症。现有方法通过分析高通量测序数据来发现结构变异。尽管这些方法的发展取得了长足进步,但其检测结构变异的准确性仍不足以用于诊断。对测序覆盖信号(即基因组中每个点的配对测序读数数量)的分析为设计结构变异检测方法提供了新的潜力,并可用作时间序列分析。基于时间序列评估算法 KNN(K-nearest neighbor)和 SAX(Symbolic Aggregation Approximation),我们开发了一种检测覆盖信号中重复模式的方法。利用人类基因组多样性项目(Human Genome Diversity Project)中包含 911 个不同种族背景个体全基因组的丰富数据集,构建了与各种结构变异类型相对应的断点附近区域覆盖信号的一般模式。利用这些模式开发了一个软件包,用于快速检测覆盖信号的异常。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Searching for Sequencing Signal Anomalies Associated with Genomic Structural Variations

Searching for Sequencing Signal Anomalies Associated with Genomic Structural Variations

Searching for Sequencing Signal Anomalies Associated with Genomic Structural Variations

Genomic structural variations (SVs) are among the main sources of genetic diversity. Structural variants as mutagens may significantly affect human health, causing hereditary diseases and cancers. Existing methods analyze high-throughput sequencing data to find structural variants. Despite substantial progress in their development, the methods still fail to detect structural variations with an accuracy sufficient for their use in diagnosis. Analysis of the sequencing coverage signal (i.e., the number of aligned sequencing reads for every point of a genome) holds the new potential for designing approaches to structural variation detection and can be used as time-series analysis. A method to detect repetitive patterns in the coverage signal was developed based on the time series-assessing algorithms KNN (K-nearest neighbor) and SAX (Symbolic Aggregation Approximation). Using the rich dataset encompassing the full genomes of 911 individuals with different ethnic backgrounds from the Human Genome Diversity Project, generalized patterns of the coverage signal were constructed for regions in the vicinity of breakpoints corresponding to various structural variant types. The patterns were used to develop a software package for fast detection of anomalies in the coverage signal.

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来源期刊
Biophysics
Biophysics Biochemistry, Genetics and Molecular Biology-Biophysics
CiteScore
1.20
自引率
0.00%
发文量
67
期刊介绍: Biophysics is a multidisciplinary international peer reviewed journal that covers a wide scope of problems related to the main physical mechanisms of processes taking place at different organization levels in biosystems. It includes structure and dynamics of macromolecules, cells and tissues; the influence of environment; energy transformation and transfer; thermodynamics; biological motility; population dynamics and cell differentiation modeling; biomechanics and tissue rheology; nonlinear phenomena, mathematical and cybernetics modeling of complex systems; and computational biology. The journal publishes short communications devoted and review articles.
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