JoVE - Journal of Visualized Experiments
JoVE Visualize
Contact Us

Nanopore sequencing-derived methylation biomarker prediction for methylation-specific PCR in patients with head and neck squamous cell carcinoma

  • 0RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany. daria.meyer@uni-jena.de.
Clinical Epigenetics +

|

September 13, 2025

|

September 13, 2025

View abstract on PubMed

Summary

This summary is machine-generated.

This study introduces a new workflow for discovering DNA methylation biomarkers using nanopore sequencing. This method efficiently identifies early cancer detection markers for head and neck squamous cell carcinoma.

Area Of Science

  • Epigenetics
  • Genomics
  • Cancer Research

Background

  • DNA methylation alterations in CpG islands are hallmarks of cancer.
  • Promoter hypermethylation of tumor-suppressor genes occurs early in cancer development.
  • Cancer-type specific methylation changes hold potential as early diagnostic biomarkers.

Purpose Of The Study

  • To develop a workflow for discovering and designing DNA methylation-specific PCR (MSP) biomarkers.
  • To leverage nanopore sequencing for identifying differentially methylated regions.
  • To create clinically relevant epigenetic assays.

Main Methods

  • Utilized nanopore sequencing on control and head and neck squamous cell carcinoma (HNSCC) tissue samples.
  • Developed a generic workflow for DNA methylation biomarker discovery and MSP primer design.
  • Validated MSP assays on a cohort of 48 HNSCC and 46 control samples.

Main Results

  • Nanopore sequencing successfully predicted differentially methylated regions between HNSCC and healthy tissues.
  • Functional MSP primers were designed based on predicted methylation patterns.
  • Four out of six designed MSP assays demonstrated high sensitivity and specificity (AUC > 0.8) in a validation cohort.

Conclusions

  • The developed DNA methylation-based workflow enables the design of adaptable, clinically relevant epigenetic assays.
  • Long-read methylation data facilitate biomarker discovery even with low sequencing coverage.
  • The workflow is effective with small initial sample sizes, supporting early cancer detection.

Keywords: