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Published on: October 5, 2012
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Targeted DNA methylation from cell-free DNA using hybridization probe capture
David N Buckley1, Gerald Gooden1, Kuan Feng2
1Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
NAR Genomics and Bioinformatics
|January 5, 2023
Summary
Hybridization probe capture using myBaits® Custom Methyl-seq kit shows high accuracy and reproducibility for cell-free DNA methylation analysis. This method is a reliable, cost-effective platform for liquid biopsies in cancer monitoring.
Area of Science:
- Biochemistry
- Genomics
- Oncology
Background:
- Cell-free DNA (cfDNA) methylation is a promising biomarker for non-invasive cancer detection and monitoring.
- DNA methylation changes are early and widespread events in tumorigenesis.
- Hybridization probe capture is a potential high-throughput method for cfDNA methylation profiling in liquid biopsies.
Purpose of the Study:
- To evaluate the performance of hybridization probe capture (myBaits® Custom Methyl-seq kit) for cell-free DNA methylation analysis.
- To assess reproducibility, scalability, and accuracy of this method using plasma samples.
- To determine the suitability of the assay for liquid biopsy applications in cancer management.
Main Methods:
- Utilized the myBaits® Custom Methyl-seq kit for hybridization probe capture.
- Analyzed 172 plasma samples and standards for cfDNA methylation profiling.
- Compared results with whole-genome bisulfite sequencing (WGBS) gold standard data.
Main Results:
- The myBaits® assay demonstrated high target recovery (>90%) and excellent reproducibility (average R² = 0.92).
- Assay performance was not negatively impacted by increasing the number of targeted regions.
- Accurately replicated WGBS beta values with an average R² of 0.79.
Conclusions:
- Custom targeted methylation sequencing with myBaits® provides a cost-effective and reliable platform.
- The method is suitable for profiling DNA methylation at specific custom regions.
- Demonstrates potential applicability for liquid biopsies in cancer monitoring.
