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Methyl-binding DNA capture Sequencing for Patient Tissues
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Pan-Cancer Detection Through DNA Methylation Profiling Using Enzymatic Conversion Library Preparation with Targeted

Alvida Qvick1, Emma Adolfsson2, Lina Tornéus3

  • 1Clinical Research Center, Faculty of Medicine and Health, Örebro University, SE-701 85 Örebro, Sweden.

International Journal of Molecular Sciences
|October 29, 2025
PubMed
Summary
This summary is machine-generated.

Circulating cell-free DNA (cfDNA) methylation patterns differ significantly between cancer patients and those with severe symptoms. This cfDNA methylation analysis shows promise as a biomarker for early cancer detection, even in complex cases.

Keywords:
cfDNAepigeneticsliquid biopsymethylationnext-generation sequencingpan-cancer

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Area of Science:

  • Biomarkers
  • Genomics
  • Oncology

Background:

  • Distinguishing cancer from severe nonspecific symptoms is clinically challenging.
  • Circulating cell-free DNA (cfDNA) methylation is an emerging area for cancer detection.

Purpose of the Study:

  • To investigate cfDNA methylation differences between cancer patients and individuals with severe, nonspecific symptoms.
  • To develop and validate a cfDNA methylation-based classifier for cancer detection.

Main Methods:

  • Plasma cfDNA methylation analysis in 229 patients (37 with cancer).
  • Utilized NEBNext workflow, Twist pan-cancer methylation panel, nf-core/methylseq, and DMRichR for analysis.
  • Developed a machine learning classifier with cross-validation and external validation.

Main Results:

  • Cancer samples exhibited higher overall CpG methylation (1.82% vs. 1.34%, p < 0.001).
  • Identified 162 differentially methylated regions (DMRs), with 95.7% hypermethylated in cancer.
  • The machine learning classifier achieved an AUC of 0.88 (83.8% sensitivity, 83.8% specificity) in the final model.

Conclusions:

  • Distinct cfDNA methylation patterns serve as a robust biomarker for cancer detection.
  • The developed classifier shows potential for identifying cancer in patients with confounding conditions.
  • cfDNA methylation analysis offers a promising non-invasive approach for early cancer diagnosis.