European Molecular Biology Laboratory, Genome Biology, Meyerhofstr. 1, 69117 Heidelberg, Germany.
Bioinformatics. 2012 Sep 15;28(18):i333-i339. doi: 10.1093/bioinformatics/bts378.
The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs.
We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity.
DELLY is available at www.korbel.embl.de/software.html
以高灵敏度和特异性发现基因组结构变异 (SV) 是描述自然发生的变异和理解个人基因组测序数据中病理体细胞重排的必要条件。特别感兴趣的是能够在单核苷酸分辨率下准确识别异质测序数据集中简单和复杂重排的综合方法，这是研究 SV 形成机制和功能后果的最佳基础。
我们开发了一种 SV 发现方法，称为 DELLY，它集成了短插入配对末端、长程 mate-pairs 和分裂读取比对，以在单核苷酸分辨率下准确描绘基因组重排。DELLY 适用于检测拷贝数可变缺失和串联重复事件，以及平衡重排，如倒位或相互易位。因此，DELLY 能够确定包括复杂事件在内的全基因组重排谱。在模拟数据上，DELLY 在广泛的测序参数范围内优于其他 SV 预测方法。在真实数据上，DELLY 可靠地从 1000 基因组计划和癌症基因组中发现 SV，并对随机选择的缺失基因座进行验证实验，显示出很高的特异性。
DELLY 可在 www.korbel.embl.de/software.html 获得。
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