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ORIGINAL RESEARCH article
Front. Epigenet. Epigenom.
Sec. Epigenomic Tools
Volume 2 - 2024 |
doi: 10.3389/freae.2024.1362926
This article is part of the Research Topic New long-read sequencing based epigenomic technologies View all articles
Benchmark of the Oxford Nanopore, EM-seq, and HumanMethylationEPIC BeadChip for detection of the 5mC sites in cancer and normal samples
Provisionally accepted- 1 Centre for Strategic Planning, Moscow, Moscow Oblast, Russia
- 2 Federal Medical & Biological Agency of Russia, Moscow, Moscow Oblast, Russia
Whole genome DNA methylation identification is crucial for profiling of the physiologically and clinically relevant epigenetic changes. Although there are multiple experimental methods, their accuracy, advantages and disadvantages need to be investigated in application to the complex tissue objects. Here we performed a benchmark of 5mC detection with Oxford Nanopore and EM-seq methods. To this end, we profiled in a genome wide manner 5mC sites in colorectal tumors and normal tissues for 3 patients and applied HumanMethylationEPIC BeadChip as an additional control approach. We estimated the whole genome scale of the methylation detection that each method yields. Our investigation describes sensitivity and specificity of each platform and impact that sequencing coverage brings. From our analysis follows higher sensitivity and specificity of the Nanopore sequencing over the EM-seq method. Moreover, ONT sequencing followed by Megalodon methylation detection demonstrates better quantitative agreement of the epigenetic signals between biological replicates. Also, our analysis highlights that with 40X and above coverage EM-seq slightly outperforms ONT and yields high accurate detection of the 5mC signals (AuPR=0.99178, AuROC=0.98161). The study has been performed for colon cancer and 1 Deinichenko et al.
Keywords: DNA Methylation, epigenetics, DNA modification, nanopore sequencing, DNA methylation detection, EM-seq
Received: 29 Dec 2023; Accepted: 10 Jun 2024.
Copyright: © 2024 Deinichenko, Vynogradskaya, Grebnev, Mikova, Bobylev, Shaymardanov, Ivashechkin, Erokhina, Akinshina, Semyanihina, Mitrofanov, Grammatikati, Yudin, Yudin, Makhotenko, Keskinov, Kraevoy, Makarova, Snigir, Svetlichnyy and Skvortsova. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Dmitry Svetlichnyy, Centre for Strategic Planning, Moscow, 119121, Moscow Oblast, Russia
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