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首页> 外文期刊>International journal of computational biology and drug design >Cross analysis of whole genome deep sequencing data reveals over-presence of nonintronic insertions and deletions (INDELs)
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Cross analysis of whole genome deep sequencing data reveals over-presence of nonintronic insertions and deletions (INDELs)

机译：对全基因组深度测序数据的交叉分析揭示了非内含子插入和缺失（INDEL）的过度存在

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摘要

The advent of high-throughput whole genome/exome sequencing has provided opportunities in studying genetic variations and diseases at the individual nucleotide level. A number of approaches have been published describing methods that align next-generation sequencing reads and identify genetic variants. However, existing variant calling and annotation algorithms have limitations in reporting true variants for an individual genome due to their insufficient functionalities and features. Given the high importance of variants that map to exons and promoters or to nonintronic variants, we developed a ranking score function (R-Score) pipeline to prioritise nonintronic variants across multiple samples or individuals by taking into consideration sequencing coverage, homozygosity, and base calling quality of identified variants. By analysing deep high-throughput sequencing data for 17 members of the Coriell CEPH/UTAH 1463 family pedigree using the R-Score pipeline, we examined the prevalence of scored nonintronic insertions and deletions (INDELs) across multiple individuals.
机译：高通量全基因组/外显子组测序的出现为研究个体核苷酸水平的遗传变异和疾病提供了机会。已经发布了许多方法，描述了对齐下一代测序读数并鉴定遗传变异的方法。然而，由于其功能和特征不足，现有的变异调用和注释算法在报告单个基因组的真实变异中有局限性。鉴于映射到外显子和启动子或非内含子变异体的重要性很高，我们开发了一种排序得分函数（R-Score）流程，通过考虑测序覆盖率，纯合性和碱基检出，在多个样本或个体中对非内含子变异体进行优先排序已识别变体的质量。通过使用R-Score管道分析Coriell CEPH / UTAH 1463家族谱系的17个成员的深层高通量测序数据，我们研究了在多个个体中计分的非内含子插入和缺失（INDEL）的普遍性。

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