DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing

By Peng Ni, Fan Nie, Zeyu Zhong, Jinrui Xu, Neng Huang, Jun Zhang, Haochen Zhao, You Zou, Yuanfeng Huang, Jinchen Li and 3 more. bioRxiv, 2023

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Long single-molecular sequencing, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, is advantageous in detecting DNA 5-methylcytosine (5mC) in CpGs, especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence PCR-treated and M.SssI-treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 AUC on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5mCs using PacBio CCS.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8d1fd139310bb4dbbd6d21f6a84dae59c97662ec