DI-tector: defective interfering viral genomes' detector for next-generation sequencing data.
DI-tector: defective interfering viral genomes' detector for next-generation sequencing data.
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DOI：
10.1261/rna.066910.118
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发表时间：
2018-10
期刊：
影响因子：
--
通讯作者：
Komarova AV
中科院分区：
文献类型：
--
作者：
Beauclair G;Mura M;Combredet C;Tangy F;Jouvenet N;Komarova AV
缺陷干扰（DI）基因组或缺陷病毒基因组（DVG）是在大多数病毒（包括活病毒疫苗）复制期间产生的截短的病毒基因组。其中，“锅柄”或复制回（cb）和“发夹”或快速回（sb）DI基因组是在RNA病毒复制过程中产生的。5′ cb/sb DI基因组与病毒发病机制高度相关，因为它们具有免疫刺激特性，可增加宿主先天免疫系统对病毒的识别。我们已经开发了DI-tector，这是一个用户友好且免费提供的程序，可以从下一代测序（NGS）数据中识别和表征cb/sb基因组。DI-tector证实了麻疹病毒（MV）感染细胞中存在5′ cb基因组。DI-tector还鉴定了一个新的5′ cb基因组，以及多种3′ cb/sb基因组，这些基因组的存在以前在MV感染的细胞中未被常规方法检测到。通过RT-qPCR和RT-PCR证实了这些新的cb/sb基因组的存在，验证了DI-tector揭示感染细胞样品中DI基因组群体的景观的能力。使用不同的实验和模拟数据集的性能评估显示了强大的特异性和灵敏度的DI-tector。我们建议DI-tector作为无偏检测DI病毒基因组的通用工具，包括5′ cb/sb DI基因组，在NGS数据。
Defective interfering (DI) genomes, or defective viral genomes (DVGs), are truncated viral genomes generated during replication of most viruses, including live viral vaccines. Among these, “panhandle” or copy-back (cb) and “hairpin” or snap-back (sb) DI genomes are generated during RNA virus replication. 5′ cb/sb DI genomes are highly relevant for viral pathogenesis since they harbor immunostimulatory properties that increase virus recognition by the innate immune system of the host. We have developed DI-tector, a user-friendly and freely available program that identifies and characterizes cb/sb genomes from next-generation sequencing (NGS) data. DI-tector confirmed the presence of 5′ cb genomes in cells infected with measles virus (MV). DI-tector also identified a novel 5′ cb genome, as well as a variety of 3′ cb/sb genomes whose existence had not previously been detected by conventional approaches in MV-infected cells. The presence of these novel cb/sb genomes was confirmed by RT-qPCR and RT-PCR, validating the ability of DI-tector to reveal the landscape of DI genome population in infected cell samples. Performance assessment using different experimental and simulated data sets revealed the robust specificity and sensitivity of DI-tector. We propose DI-tector as a universal tool for the unbiased detection of DI viral genomes, including 5′ cb/sb DI genomes, in NGS data.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
5.4
作者：
Finke, S;Conzelmann, KK
通讯作者：
Conzelmann, KK
影响因子：
9.4
作者：
Ohtsuru, Shigeru;Ueda, Yoshihide;Chiba, Tsutomu
通讯作者：
Chiba, Tsutomu
影响因子：
6.7
作者：
Ke R;Aaskov J;Holmes EC;Lloyd-Smith JO
通讯作者：
Lloyd-Smith JO
影响因子：
5.4
作者：
Lopez, Carolina B.
通讯作者：
Lopez, Carolina B.