CRISPR-DA: Adapting CRISPR gRNA design for detection assays

Abstract

CRISPR-Cas systems offer a viable alternative to traditional detection and diagnosis methods. However, their effectiveness relies heavily on the selection of appropriate guide RNA sequences. Existing gRNA design tools were primarily developed for gene editing and are not always directly applicable to CRISPR-based detection assays. In particular, alignmentbased methods are still used to estimate gRNA specificity, even though they can miss a substantial portion of off-target sites. In this work, we introduce CRISPR-DA, a CRISPR gRNA design tool for detection assays. We show that it provides a better assessment of gRNA specificity than BLAST, which detected only 33.27 % and 0.43 % of cross-species off-targets in two datasets. Additionally, CRISPR-DA ran two and six times faster than BLAST on these datasets, respectively. Our method incorporates advances from gene-editing guide RNA design tools, including uncertainty-informed guide RNA design, to improve the selection of guides with high on-target activity. CRISPR-DA is available at https://github.com/bmds-lab/CRISPR-DA.