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

Date
2024-12
Language
American English
Embargo Lift Date
Department
Committee Chair
Degree
M.S.
Degree Year
2024
Department
Biostatistics
Grantor
Indiana University
Journal Title
Journal ISSN
Volume Title
Found At
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.

Description
IUI
item.page.description.tableofcontents
item.page.relation.haspart
Cite As
ISSN
Publisher
Series/Report
Sponsorship
Major
Extent
Identifier
Relation
Journal
Source
Alternative Title
Type
Thesis
Number
Volume
Conference Dates
Conference Host
Conference Location
Conference Name
Conference Panel
Conference Secretariat Location
Version
Full Text Available at
This item is under embargo {{howLong}}