Integrating allele-specific PCR with CRISPR-Cas13a for sensitive KRAS mutation detection in pancreatic cancer

Abstract

Abstract Background The clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas13a system has strong potential for highly sensitive detection of exogenous sequences. The detection of KRAS G12 point mutations with low allele frequencies may prove powerful for the formal diagnosis of pancreatic ductal adenocarcinoma (PDAC). Results We implemented preamplification of KRAS alleles (wild-type and mutant) to reveal the presence of mutant KRAS with CRISPR-Cas13a. The discrimination of KRAS G12D from KRAS WT was poor for the generic KRAS preamplification templates and depended on the crRNA design, the secondary structure of the target templates, and the nature of the mismatches between the guide and the templates. To improve the specificity, we used an allele-specific PCR preamplification method called CASPER (Cas13a Allele-Specific PCR Enzyme Recognition). CASPER enabled specific and sensitive detection of KRAS G12D with low DNA input. CASPER detected KRAS mutations in DNA extracted from patients’ pancreatic ultrasound-guided fine-needle aspiration fluid. Conclusion CASPER is easy to implement and is a versatile and reliable method that is virtually adaptable to any point mutation.

Keywords

• CRISPR
• Cas13a
• KRAS
• Pancreatic cancer
• Liquid biopsy