Cont-ID:检测病毒元基因组数据中的样本交叉污染
Johan Rollin1,2, Wei Rong1, Sébastien Massart3
1Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium.
BMC biology
|October 14, 2023
概括
高通量测序 (HTS) 提供敏感的病毒检测,但需要管理交叉污染. 该Cont-ID工具准确地区分真实病毒感染与污染,提高诊断可靠性.
科学领域:
- 分子诊断学 分子诊断学
- 生物信息学是一种生物信息学.
- 病毒学 病毒学
背景情况:
- 高通量测序 (HTS) 是一种强大的病毒检测技术,由于其灵敏度和可重复性,它有可能超越PCR方法.
- 交叉污染,即样本之间的遗传物质交换,对敏感的HTS方法构成了挑战,需要严格的监测.
- 建立一个可靠的检测门,以估计的交叉污染为基础,对于基于HTS的精确病毒诊断至关重要.
研究的目的:
- 引入Cont-ID,这是一个用于检测HTS数据集中的交叉污染的生物信息工具.
- 评估Cont-ID在区分真实病毒感染与交叉污染方面的准确性.
- 提供一种方法,以提高对基于HTS的病毒检测结果的信心.
主要方法:
- Cont-ID分析了病毒测序在并行处理的样本中的相对丰富性和重复性.
- 该工具需要至少一个特定的外部控制,称为外星控制,进行分析.
- 验证涉及273个真实数据集,涵盖68个病毒物种和各种图书馆准备协议.
主要成果:
- 在将病毒检测归类为真实感染或交叉污染时,Cont-ID实现了91%的准确性.
- 该工具在各种主机 (果树,植物,人类) 和图书馆类型中表现出有效性.
- Cont-ID通过优先考虑需要确认的结果来促进下游解释.
结论:
- 当使用外来控制时,Cont-ID有效地监测和突出显示HTS病毒检测中的交叉污染,特别是使用Illumina技术.
- 灵活的方法依赖于对测序读数和批量特定污染模式的生物信息学分析.
- 在常规实施之前,Cont-ID可适应实验室优化和验证.
相关概念视频
Methods to Assess Microbial Communities
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Human Virome
The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible only with...
Rapid Identification of Pathogens
MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...


