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Updated: Jan 12, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens.

Keisuke Kunigo¹, Satoi Nagasawa¹, Keiko Kajiya¹

¹Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.

Cell Reports Methods

|November 4, 2025

Summary

This summary is machine-generated.

We developed t-nanoEM, a new method for precise DNA methylation analysis using long-read sequencing. This technique enhances cancer research by revealing haplotype-aware methylation patterns and spatial gene expression links.

Keywords:

CP: molecular biology DNA methylation allele-specific methylation breast cancer long-read sequencing lung cancer nanopore sequencing phasing analysis target sequencing

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Last Updated: Jan 12, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients

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Published on: June 16, 2017

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

Genomics
Molecular Biology
Cancer Research

Background:

Accurate detection of DNA methylation patterns is crucial for understanding various biological processes, including cancer development.
Existing long-read DNA sequencing methods require efficient target enrichment strategies for precise methylation analysis.

Purpose of the Study:

To establish a practical and efficient target enrichment method for long-read DNA sequencing to detect precise DNA methylation patterns.
To apply this method for comprehensive methylation analysis in cancer research.

Main Methods:

Development of t-nanoEM, integrating hybridization-based capture with long-read enzymatic methyl sequencing (EM-seq) library preparation.
Utilizing nanopore sequencing for high-coverage, long-read DNA analysis.
Application of the method to breast and lung cancer samples.

Main Results:

Achieved high sequencing coverage (up to ×570) with a 5 kb N50 length, enabling detailed methylation detection.
Demonstrated haplotype-aware display of DNA methylation signature changes in local cell populations using breast cancer data.
Observed potential associations between spatial gene expression diversity and DNA methylation changes in lung cancer.

Conclusions:

t-nanoEM provides an efficient approach for high-resolution, long-read DNA methylation analysis.
The method facilitates the study of cancer epigenetics, revealing complex methylation patterns in a haplotype-aware manner.
This technique offers new insights into the relationship between DNA methylation and spatial gene expression in various cancers.