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Updated: Sep 22, 2025
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Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
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Single-Molecule Sequencing Enables Long Cell-Free DNA Detection and Direct Methylation Analysis for Cancer Patients
L Y Lois Choy1,2,3,4, Wenlei Peng1,3,4, Peiyong Jiang1,2,3,4
1Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
Clinical Chemistry
|May 19, 2022
Summary
Single-molecule sequencing revealed a novel population of long circulating tumor DNA (ctDNA) in cancer patients. Analyzing ctDNA length and methylation patterns significantly improves cancer detection accuracy for liquid biopsies.
Area of Science:
- Oncology
- Genomics
- Biotechnology
Background:
- Circulating tumor DNA (ctDNA) analysis is crucial for cancer care.
- Conventional methods focus on short DNA fragments and degrade DNA, hindering long DNA analysis.
- Single-molecule sequencing offers a novel approach to overcome these limitations.
Purpose of the Study:
- To investigate the utility of single-molecule sequencing for analyzing long plasma DNA fragments.
- To assess the diagnostic potential of long cell-free DNA (cfDNA) and its methylation patterns in cancer detection.
- To develop a methylation score for improved hepatocellular carcinoma (HCC) detection.
Main Methods:
- Employed Single-molecule real-time (SMRT) sequencing to analyze plasma DNA.
- Performed fragment size and direct methylation analysis on individual DNA molecules.
- Developed and utilized an HCC methylation score based on single-molecule methylation patterns.
Main Results:
- Identified a substantial population of long plasma DNA (>1 kb), with the longest molecule reaching 39.8 kb in HCC patients.
- Tumoral cfDNA was generally shorter and exhibited lower methylation levels than nontumoral cfDNA.
- Long cfDNA molecules significantly enhanced cancer detection discriminatory power (AUC: 0.91) compared to short cfDNA (AUC: 0.75).
Conclusions:
- Revealed a previously undetected population of long cfDNA in cancer patients.
- Direct methylation analysis of these long cfDNA molecules offers new avenues for cancer liquid biopsy.
- This approach enhances the potential for non-invasive cancer detection and monitoring.
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