CasCADE: Cas-CRISPR Automated Design and Evaluation for targeted gRNA detection assays

The adaptation of CRISPR technologies for molecular detection marks a significant advancement in the field of biosurveillance and infectious disease response. CRISPR-based detection systems offer superior specificity and sensitivity compared to traditional PCR methods by directly binding and cleaving target DNA or RNA sequences, thus signaling the presence of specific pathogens. These advantages include the elimination of non-specific amplification and the reduction of required genetic material, leading to faster time to results without the need for extensive amplification cycling. However, the efficacy of CRISPR technologies heavily depends on the design of specific guide RNA (gRNA) sequences tailored for each genomic target, a process that can be intricate and time-consuming. We present Cas-CRISPR Automated Design and Evaluation (CasCADE), a state-of-the-art gRNA design software platform with a high degree of flexibility and modularity. CasCADE incorporates k-mer set operations to reduce time to answer for large data inputs when compared to computationally costly multiple sequence alignment methodologies and uses an agnostic whole genome approach to maximize gRNA discovery. CasCADE can be scaled efficiently to problems of any input sequence size and can be used for design, candidate evaluation, or both, depending on user need.

This work describes our software pipeline Cas-CRISPR Automated Design and Evaluation (CasCADE) that allows for in silico design of Cas-CRISPR detection assays. We demonstrate the viability of our design process in the lab and report 15 successful designs across nine diverse target organisms. The rapid time to answer afforded by CasCADE, combined with the superior specificity and sensitivity offered by emergent CRISPR detection assays compared to traditional PCR methods, makes this a timely contribution to pandemic preparedness and biosurveillance interests.