评估元基因组学和针对病毒诊断和监测的有针对性的方法
Sarah Buddle1, Leysa Forrest2, Naomi Akinsuyi1
1Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
Genome medicine
|September 9, 2024
概括
使用向丰富或牛津纳米孔技术 (ONT) 的元基因组测序显示出对病原体检测的希望. 向丰富显著提高对低病毒载荷的敏感性,而ONT提供实时分析,方法选择取决于临床需要.
科学领域:
- 基因组医学是基因组医学.
- 传染病诊断 传染病诊断 传染病诊断
- 生物信息学是一种生物信息学.
背景情况:
- 甲基因组学对于识别新型病原体至关重要,但在诊断环境中面临着挑战.
- 目前的Illumina短读工作流需要很高的测序深度,并且有很长的周转时间.
- 牛津纳米孔技术 (ONT) 和有针对性的测序为提高灵敏度和速度提供了潜在的解决方案.
研究的目的:
- 评估使用Illumina和ONT进行非向测序,并使用Twist生物科学综合病毒研究小组 (CVRP) 进行向测序.
- 评估这些方法在模拟的临床样本中检测病毒的性能,这些样本具有低病毒丰度和高宿主含量.
- 为了比较不同分类学分类器对元基因组学分析的有效性.
主要方法:
- 评估了非定位的Illumina和ONT元基因组工作流.
- 通过使用Twist CVRP (针对3153种病毒) 评估基于Illumina的有针对性的丰富方法.
- 在人类DNA/RNA背景中测试了六种病毒模拟社区的稀释系列.
主要成果:
- 扭曲CVRP提高了10-100倍的灵敏度,可以检测低病毒载量 (60个基因组拷贝/毫升).
- 与Illumina相比,非向的ONT在高病毒负载时表现出良好的敏感性,但在较低负载时需要更长的运行时间.
- 非定位的ONT提供了比非定位的Illumina更好的特异性;强大的值标准化了分类器的结果.
结论:
- 甲基因组学正在向病原体发现诊断的标准护理方向迈进.
- 非定向的Illumina,ONT和定向的CVRP方法在灵敏度,特异性,速度和成本方面具有明显的优势.
- 最佳的元基因组学方法取决于具体的临床应用和诊断要求.
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