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Updated: Dec 21, 2025
Comparative Lesions Analysis Through a Targeted Sequencing Approach
Published on: November 5, 2019
Detection of Microsatellite Instability from Circulating Tumor DNA by Targeted Deep Sequencing
Zhenghao Cai1, Zhenxin Wang2, Chenglin Liu3
1Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China; Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, People's Republic of China.
A new blood test accurately detects microsatellite instability (MSI) in cancer patients, even with low levels of circulating tumor DNA (ctDNA). This breakthrough improves upon tissue-based testing limitations, offering a more accessible diagnostic tool for high MSI (MSI-H) detection.
Area of Science:
- Oncology
- Genetics
- Molecular Diagnostics
Background:
- Microsatellite instability (MSI) detection is crucial for cancer diagnosis and treatment selection.
- Current MSI detection methods rely on tissue biopsies, which can be invasive and require sufficient tumor content.
- Detecting MSI from blood (liquid biopsy) is challenging due to low circulating tumor DNA (ctDNA) concentrations and limited sensitivity.
Purpose of the Study:
- To develop and validate a novel next-generation sequencing (NGS)-based algorithm for detecting MSI from blood samples.
- To overcome the sensitivity limitations of previous blood-based MSI detection methods.
- To establish a non-invasive method for identifying high microsatellite instability (MSI-H) status.
Main Methods:
- Developed a "blood MSI signature enrichment analysis" algorithm using NGS.
- Identified and extracted marker sites distinguishing MSI-H from microsatellite stable (MSS) tumors.
- Employed hypergeometric probability to assess MSI status based on read coverage patterns in plasma ctDNA compared to white blood cells.
- Validated the algorithm using in vitro dilution experiments, in silico simulations, and an independent cohort of 87 colorectal cancer patients.
Main Results:
- The algorithm demonstrated high sensitivity and specificity in detecting MSI from ctDNA.
- Achieved 98% sensitivity and 100% specificity at 1% ctDNA and 91.8% sensitivity at 0.4% ctDNA in simulation experiments.
- In an independent validation cohort, the method achieved 94.1% sensitivity and 100% specificity for samples with ctDNA >0.4%.
Conclusions:
- The developed blood MSI signature enrichment analysis is a sensitive and specific method for detecting MSI from blood.
- This NGS-based approach offers a promising non-invasive alternative to tissue-based MSI testing.
- The algorithm has the potential to improve accessibility and enable earlier detection of MSI-H in cancer patients.
