Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
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DOI：
10.1038/s41467-020-16481-5
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发表时间：
2020-06-10
影响因子：
16.6
通讯作者：
Frazer, Kelly A.
中科院分区：
文献类型：
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作者：
Jakubosky, David;Smith, Erin N.;Frazer, Kelly A.
结构变异(SVS)和短串联重复序列(STR)是遗传多样性的重要来源，但由于它们难以准确识别和分型，在遗传学研究中没有进行常规分析。由于SVS和STR的大小和类型各不相同，因此有必要应用多种算法，结合来自测序数据的不同类型的证据，并采用复杂的过滤策略来发现一套全面的高质量和可重复的变种。在这里，我们收集了一组来自477个不同个体的719个深度全基因组测序(WGS)样本(平均为42x)，我们使用五种算法发现了广泛的SV和STR变体并对其进行了基因分型。我们使用177对独特的遗传重复来识别影响变异呼叫重复性的因素，并开发出系统的过滤策略，以创建迄今为止最完整和最具特征化的SVS和STR图谱之一。
Structural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assemble a set of 719 deep whole genome sequencing (WGS) samples (mean 42x) from 477 distinct individuals which we use to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We use 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and develop a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.