高通量测序的多富集方法研究人类癌症中的病毒。
High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.
机构信息
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark.
Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
出版信息
J Infect Dis. 2019 Sep 13;220(8):1312-1324. doi: 10.1093/infdis/jiz318.
BACKGROUND
Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data.
METHODS
In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads.
RESULTS
Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.
CONCLUSIONS
Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
背景
病毒和其他传染性病原体导致超过 15%的人类癌症病例。基于高通量测序的病毒-癌症相关性研究主要集中在癌症转录组数据上。
方法
在这项研究中，我们应用了多种针对主要病毒群的预测序富集方法，对来自 18 种癌症来源样本类型的 197 个样本中的病毒进行了特征分析。我们使用高通量测序生成了 710 个数据集，包含 570 亿个测序读段。
结果
对从头组装的 contigs 和单个测序读段中的病毒内容进行详细的计算机分析，包括排除病毒假象，得到了检测到的病毒图谱。我们的数据显示，乳头瘤病毒、圆环病毒、疱疹病毒和细小病毒主导了病毒组。超过一半的样本包含 1 种或多种病毒；然而，没有发现特定病毒与癌症类型之间的联系。
结论
我们的研究揭示了癌症中病毒的存在，并为未来提供了高度相关的病毒组数据。
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