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Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Detecting DNA cytosine methylation using nanopore sequencing.

Jared T Simpson^1,2, Rachael E Workman³, P C Zuzarte¹

¹Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

|February 21, 2017

Summary

This summary is machine-generated.

This study quantifies how 5-methylcytosine (5-mC) DNA base modifications affect nanopore sequencing signals. A new method accurately detects 5-mC in human DNA methylomes without special library prep.

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Methodology for Accurate Detection of Mitochondrial DNA Methylation

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Published on: May 20, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Nanopore sequencing devices generate electrical current signals sensitive to DNA base modifications.
5-methylcytosine (5-mC) is a critical epigenetic modification influencing gene expression.

Purpose of the Study:

To quantify the effect of 5-methylcytosine on electrolytic current signals in the Oxford Nanopore Technologies MinION sequencer.
To develop a computational method for distinguishing 5-mC from unmethylated cytosine using nanopore sequencing data.

Main Methods:

Utilized synthetically methylated DNA for model training.
Developed and applied a hidden Markov model to analyze nanopore sequencing data.
Sequenced the human DNA methylome without specialized library preparation steps.

Main Results:

Successfully quantified the signal changes associated with 5-mC on the MinION platform.
The hidden Markov model accurately distinguished between methylated and unmethylated cytosine.
Enabled direct sequencing of the human methylome from native DNA.

Conclusions:

Nanopore sequencing signals provide a reliable readout for 5-mC detection.
The developed hidden Markov model is effective for methylome sequencing.
This method simplifies and enhances the study of DNA methylation patterns.