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Smart-SNPer: Automated crRNA design for ultrasensitive RPA-Cas12a SNP detection
Liya Han1, Wenjun Feng1, Lv Wang1
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
Biosensors & Bioelectronics
|August 27, 2025
Summary
Smart-SNPer simplifies single-nucleotide polymorphism (SNP) detection for precision medicine. This automated tool enables rapid, field-deployable SNP genotyping with high accuracy, even for low-abundance mutations.
Area of Science:
- Biotechnology
- Genomics
- Molecular Diagnostics
Background:
- Single-nucleotide polymorphism (SNP) detection is crucial for precision medicine.
- Current methods are often complex and unsuitable for resource-limited settings.
- There is a need for accessible and efficient SNP detection tools.
Purpose of the Study:
- To introduce Smart-SNPer, a novel, automated tool for designing CRISPR-based SNP detection assays.
- To develop a user-friendly, structure-guided crRNA design platform.
- To enable rapid and accurate SNP detection in resource-limited and point-of-care settings.
Main Methods:
- Developed Smart-SNPer, a one-click, structure-guided crRNA design tool.
- Automated the design of Recombinase Polymerase Amplification (RPA)-Cas12a assays (CORDSv2).
- Engineered a specific CORDSv2 assay for the NRAS:g.648C>A SNP.
Main Results:
- Smart-SNPer achieved 96% target coverage and optimized crRNA design for specificity.
- The NRAS assay detected 0.1% mutant alleles with minimal input DNA (20 ng).
- 100% concordance with Next-generation sequencing (NGS) was observed in 27 clinical samples, with a linear semiquantitative response.
Conclusions:
- Smart-SNPer facilitates the development of highly specific and sensitive SNP detection assays.
- The automated workflow is field-deployable, providing results within 1 hour.
- This technology bridges the gap between advanced SNP diagnostics and point-of-care applications, enhancing precision medicine accessibility.
