Comparing Nanopore to MethylationEPIC Array and EM-Seq in DNA Methylation Detection

Abstract

DNA Methylation is an important biological process in epigenetics, and many methods have been developed to profile DNA methylation. Recently a growing number of studies use Nanopore long-read sequencing technology in DNA methylation detection, in contrast to widely used Infinium arrays and short-read whole genome sequencing (WGS) methods. In this study, we evaluate the performance of Nanopore sequencing in DNA methylation detection by comparing it to the Illumina MethylationEPIC microarray (EPIC) and Enzymatic Methyl-Sequencing. We first compare Oxford Nanopore Technologies’ Nanopore with MethylationEPIC array. Among the ~850,000 CpG sites covered by both methods, we observed high concordance (R ≥ 0.94 across all four samples). After downsampling Nanopore data from an average coverage of 26.6 reads per site to 10 reads per site, the correlation in CpG methylation remained high (R≥ 0.935). Next, we compare Nanopore with EM-Seq in the context of low coverage. The lower CpG methylation correlation (R ≥ 0.8), can be attributed to reduced coverage of hypomethylated CpG sites by EM-Seq. Furthermore, we highlight Nanopore’s unique capabilities, including native DNA sequencing that can differentiate modification types and the use of long reads for haplotype phasing. Overall, Nanopore demonstrated high concordance with the EPIC array and more uniform coverage across the genome than EM-Seq. This study provides insights for researchers in selecting appropriate DNA methylation detection methods, considering factors such as cost, DNA input, and the complexity of downstream analysis.