CRISPR-based SNP detection technologies advance from classical methods to cutting-edge innovations

Abstract

Single nucleotide polymorphisms (SNPs) constitute the most prevalent form of genetic variations, critically influencing human disease susceptibility, drug response, and pathogen evolution. Conventional SNP detection methods, however, face significant limitations: they often lack the necessary balance of precision, speed, and deployability required for diverse applications, ranging from point-of-care clinical diagnostics to rapid pathogen surveillance. The advent of CRISPR/Cas systems, particularly the discovery of the trans-cleavage activity of Cas nucleases, has revolutionized this field by offering unparalleled single-nucleotide specificity, isothermal operation, and signal amplification capabilities. In this review, we first systematically examine the foundational CRISPR-based SNP detection platforms, with a focused analysis of pioneering systems including SHERLOCK, HOLMES, and Cas14-DETECTR. Subsequently, we delve into the transformative technical advancements that have propelled these platforms towards cutting-edge innovations, emphasizing three critical pathways: (1) novel strategies for achieving ultra-high specificity in single-nucleotide discrimination, (2) breakthroughs in overcoming protospacer adjacent motif (PAM) sequence constraints, and (3) innovative approaches for optimizing sensitivity to meet stringent clinical detection thresholds. Finally, we critically evaluate the persistent challenges hindering the widespread adoption of current CRISPR-based SNP detection frameworks and propose actionable research trajectories aimed at advancing CRISPR technologies for high-precision SNP genotyping. This review provides a comprehensive overview of the remarkable evolution of CRISPR-based SNP detection, from its classical origins to its current status as a frontier innovation. It also sheds light on future directions essential for realizing the full potential of CRISPR as a transformative tool in precision medicine and global health surveillance.