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对纳米孔测序进行批判性评估,以检测多种形式的DNA修饰

Yimeng Kong^1,2, Yanchun Zhang¹, Edward A Mead¹

¹Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

bioRxiv : the preprint server for biology

|November 28, 2024

概括

纳米孔测序可靠地绘制出像5-甲基细胞素 (5mC) 这样丰富的DNA修饰,但与低丰富的DNA修饰作斗争,产生错误的阳性. 使用虚假发现率和控制的新框架有助于准确的DNA修饰分析.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

纳米孔测序是一种用于DNA修饰映射的强大工具.
在DNA修饰检测中,假阳性调用会导致错误的生物学解释.

研究的目的:

为严格评估用于检测DNA修饰的纳米孔测序提出一个框架.
评估纳米孔测序在各种DNA修饰和丰度中的可靠性.

主要方法:

开发了一个使用虚假发现率 (FDR) 分析的框架.
整合了合理设计的负控来捕捉背景和混的修改.
在不同的位置和丰度上对多个DNA修饰 (5mC,5hmC,6mA) 的纳米孔测序性能进行了批判性评估.

主要成果:

纳米孔测序显示,对于丰富的修饰,如CpG位点上的5-甲基细胞因子 (5mC) 和哺乳动物脑细胞中的5-基甲基细胞因子 (5hmC) 的高可靠性.
对于低丰度的修饰,观察到显著的错误阳性检测,包括5mC在CpH位点,5hmC和N6-甲基脱氧氨 (6mA) 在大多数哺乳动物细胞类型中.
性能根据修改丰度和基因组背景而有很大差异.

结论:

严格的评估框架对于使用纳米孔测序进行准确的DNA修饰分析至关重要.
未来的方法开发和生物研究应该纳入这个框架.
优先考虑纳米孔测序对于生物医学应用中的高丰度修饰,因为潜在的虚假阳性与低丰度目标.

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