AnnotSV: an integrated tool for structural variations annotation
AnnotSV: an integrated tool for structural variations annotation
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DOI：
10.1093/bioinformatics/bty304
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发表时间：
2018-10-15
期刊：
影响因子：
5.8
通讯作者：
Muller, Jean
中科院分区：
文献类型：
--
作者：
Geoffroy, Veronique;Herenger, Yvan;Muller, Jean
结构变异（SV）是人类基因组变异的主要来源，在进化过程中塑造了其实际结构。此外，许多人类疾病是由SV引起的，这突出了准确检测这些基因组事件的需要，但也需要注释它们并帮助它们的生物学解释。因此，我们开发了AnnotSV，它汇编了功能、监管和临床相关信息，旨在提供有助于（i）解释SV潜在致病性和（ii）过滤SV潜在假阳性的注释。特别是，AnnotSV报告了所分析患者的单核苷酸变异（SNV）的杂合和纯合计数以及每个SV内调用的小插入/缺失，该基因组信息对于支持或质疑SV的存在非常有用。我们还报道了相对于来自DGV的重叠变体计算的等位基因频率（MacDonald等人，2014年），这是特别强大的过滤出常见的SV。为了描述AnnotSV的强度，我们在不到60秒的时间内注释了来自1000个基因组计划的一个样品的4751个SV，整合了400万个SNV/indel的样品信息。
Structural Variations (SV) are a major source of variability in the human genome that shaped its actual structure during evolution. Moreover, many human diseases are caused by SV, highlighting the need to accurately detect those genomic events but also to annotate them and assist their biological interpretation. Therefore, we developed AnnotSV that compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to (i) interpret SV potential pathogenicity and (ii) filter out SV potential false positive. In particular, AnnotSV reports heterozygous and homozygous counts of single nucleotide variations (SNVs) and small insertions/deletions called within each SV for the analyzed patients, this genomic information being extremely useful to support or question the existence of an SV. We also report the computed allelic frequency relative to overlapping variants from DGV (MacDonald et al., 2014), that is especially powerful to filter out common SV. To delineate the strength of AnnotSV, we annotated the 4751 SV from one sample of the 1000 Genomes Project, integrating the sample information of four million of SNV/indel, in less than 60 s.