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使用PacBio循环共识测序检测DNA5甲基氨酸和甲基化分相

Peng Ni^1,2,3, Fan Nie^1,2,3, Zeyu Zhong^1,3

¹School of Computer Science and Engineering, Central South University, Changsha, 410083, China.

Nature communications

|July 8, 2023

概括

我们开发了ccsmeth,这是一个深度学习工具,用于使用PacBio循环共识测序 (CCS) 读取精确的DNA5甲基细胞素 (5mCpC) 检测. 这种方法增强了重复区域的甲基化分析,并提供了对单 haplotype 意识的见解.

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.
生物信息学是一种生物信息学.

背景情况:

像PacBio CCS和纳米孔测序等长期读取的测序技术显示出检测DNA5-甲基细胞素 (5mCpG) 的前景.
目前用于5mCpG检测的PacBio CCS方法缺乏准确性和稳定性,特别是在复杂的基因组区域.

研究的目的:

开发一种新的深度学习方法,ccsmeth,用于使用PacBio CCS读取的DNA5mCpG的准确和强大的检测.
从CCS数据创建一个Nextflow管道,ccsmethphase,用于从CCS数据中对哈普类型有意识的甲基化检测.

主要方法:

使用PacBio CCS训练的ccsmeth从聚合酶链反应处理和M.SssI-甲基转移酶处理的人类DNA中读取.
评估了ccsmeth在单分子分辨率下检测5mCpG的性能,使用长时间的CCS读数 (≥10 Kb).
开发了ccsmethphase管道用于表型感知甲基化分析,并使用中国家族三组进行了验证.

主要成果:

对于单分子5mCpG检测,ccsmeth实现了0.90准确度和0.97曲线下的面积.
全基因组站点级分析显示>0.90与二硫酸盐和纳米孔序列的相关性,仅使用10×CCS读数.
ccsmethphase成功检测出对单 haplotype 有意识的甲基化模式.

结论:

ccsmeth提供了一种强大而准确的深度学习方法,用于使用PacBio CCS长读数检测DNA 5mCpG.
ccsmethphase能够进行敏感的单元型感知甲基化分析,从而推进表观遗传学研究.
这些工具为DNA甲基化分析提供了显著的改进,特别是在具有挑战性的基因组领域.

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