Related Experiment Video
Updated: Aug 2, 2026
08:23
Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions
Published on: September 25, 2018
14.1K
Suppression Probe Enrichment for Highly Sensitive and Multiplexed Detection of RAS Mutations in Colorectal Cancer
Xinglei Su1,2,3, Yunpei Si1,4, Wenle Huang4
1The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, National Center for Translational Medicine, Shanghai 200030, China.
Analytical Chemistry
|March 12, 2026
Summary
A new ultrasensitive method called suppression probe enrichment (SPE) enables rapid and cost-effective detection of RAS mutations in cancer. This approach significantly improves upon next-generation sequencing (NGS) for guiding targeted therapies.
Area of Science:
- Molecular Biology
- Genetics
- Oncology
Background:
- RAS mutations are crucial biomarkers in cancer, particularly colorectal cancer (CRC).
- Current detection methods like next-generation sequencing (NGS) face limitations including high cost, long turnaround times, and significant sample volume requirements.
- Ultrasensitive detection of low-frequency RAS mutations is critical for effective clinical management and targeted therapy selection.
Purpose of the Study:
- To develop and validate a novel, ultrasensitive assay for detecting RAS mutations.
- To compare the performance of the new assay against conventional methods, specifically NGS.
- To establish a cost-effective and rapid method for clinical RAS genotyping in CRC.
Main Methods:
- Development of suppression probe enrichment (SPE), a method integrating thermodynamically driven enrichment with multiplex TaqMan probes.
- The SPE assay was designed to cover 286 mutation types across KRAS, HRAS, and NRAS genes.
- Validation using 57 tissue and 83 blood CRC samples, with comparison to NGS, and analysis of 30 paired tissue-plasma samples.
Main Results:
- The SPE assay demonstrated a 20-fold sensitivity improvement, with a limit of detection as low as 0.05% variant allele frequency.
- SPE reduced detection time by approximately 7-fold and costs by 3 orders of magnitude compared to NGS, requiring only 1 mL of plasma.
- High concordance rates were achieved: 93.8% positive concordance and 100% true negative rate against NGS in CRC samples. Paired sample analysis showed 93.33% overall and 86.67% positive concordance.
Conclusions:
- Suppression probe enrichment (SPE) offers a highly sensitive, rapid, and cost-effective alternative for RAS mutation detection.
- SPE is suitable for clinical RAS genotyping in colorectal cancer, aiding in the guidance of targeted therapies.
- This technology has the potential to significantly improve patient management and treatment strategies in oncology.
