使用牛津纳米孔技术纳米孔测序平台的细菌甲基组分析的可复制性和准确性
Taylor Schababerle1, Omar Hayat1, Jaeone Jung1
1Graduate Program in Diagnostic Genetics & Genomics, The University of Texas MD Anderson Cancer Center-School of Health Professions, Houston, TX, USA.
Microbial genomics
|November 19, 2025
概括
牛津纳米孔技术 (ONT) 能够直接进行甲基组分析. 只有ONT的分析是准确的,并且可以在运营商之间重现,测序覆盖率是网站一致性的关键.
科学领域:
- 基因组学就是基因组学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 微生物学 微生物学
背景情况:
- 牛津纳米孔技术 (ONT) 提供直接的甲基组分析.
- 仅对ONT与混合组合基准基甲基化调用的比较性能,特别是运营商间的可变性,还未得到研究.
研究的目的:
- 为了比较ONT-only和混合组件的基于参考的甲基化调用.
- 为了评估甲基化概况的运营商间变异性.
- 评估ONT-only甲基形状分析的准确性和可重复性.
主要方法:
- 六个运营商为纳米孔和Illumina MiniSeq平台准备了测序库.
- 有两种 *Streptococcus dysgalactiae* 的亚种. 使用了 *equisimilis* 菌株 (UT9728,UT10237).
- 使用MicrobeMod v.1.0.3识别了甲基化和图案配置文件,其中包括混合参考组件 (HRA) 和ONT-only参考组件 (ORA).
主要成果:
- 在HRA和ORA之间,动机识别一致性超过了99.9%.
- 大多数图案的可复制性很高 (Pearson的*r*>0.989对于HRAs,*r*>0.993对于ORAs),而变性图案的可复制性较低.
- 与基于HRA的调用相比,仅在ONT的甲基化站点调用显示出极好的精度和回忆 (F1得分>99.999%) .
- 不一致的甲基化部位很少见,并且与低测序覆盖率 (<70×) 相关.
结论:
- 只有ONT的甲基组分析是准确的,并且可以在各个运营商中复制.
- 测序覆盖率是影响站点级一致性的主要因素.
- 这种方法为直接的甲基组分析提供了一种可靠的方法.
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