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A Systematic Method to Detect Next-Generation Sequencing-Based Microsatellite Instability in Plasma Cell-Free DNA:
Fengchang Huang1, Lili Zhao2, Hongyu Xie2
1Kunming Medical University, Kunming, China; Department of Surgical Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China.
The Journal of Molecular Diagnostics : JMD
|December 26, 2024
Summary
A new method, plasmaMSI, enables accurate detection of microsatellite instability (MSI) in blood plasma cell-free DNA (cfDNA). This breakthrough improves upon tissue-based testing, offering a more convenient and effective biomarker for cancer patients.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genetics
Background:
- Microsatellite instability (MSI) is a key cancer biomarker, typically assessed via tumor tissue.
- Obtaining tumor tissue is invasive, creating a need for less invasive alternatives like blood plasma.
- Detecting MSI in plasma cell-free DNA (cfDNA) is challenging due to low signal-to-noise ratios.
Purpose of the Study:
- To introduce plasmaMSI, a novel method for accurate MSI detection in cfDNA.
- To overcome the technical hurdles of cfDNA-based MSI analysis.
- To provide a clinically viable alternative to tissue-based MSI testing.
Main Methods:
- Developed plasmaMSI with stringent locus selection criteria for sequencing compatibility.
- Implemented a novel deduplication strategy to enhance signal-to-noise ratio.
- Utilized a customized MSI calling algorithm adapting to individual sample duplication rates.
Main Results:
- Achieved a limit of detection of 0.15% in analytical validation using diluted cell line samples.
- Demonstrated high concordance with tissue MSI-PCR in gastrointestinal cancer patients (92.9% positive, 100% negative agreement).
- plasmaMSI addresses critical cfDNA MSI detection challenges unmet by existing methods.
Conclusions:
- plasmaMSI offers a highly accurate and validated method for cfDNA-based MSI detection.
- The method provides a more accessible and convenient approach compared to traditional tissue biopsy.
- plasmaMSI is ready for clinical application, aiding cancer patient management.
