PathoGD: an integrative genomics approach for CRISPR-based target design of rapid pathogen diagnostics

Low, S. J.; O'Neill, M.; Kerry, W. J.; Wild, N.; Krysiak, M.; Nong, Y.; Azzato, F.; Hor, E.; Williams, L.; Taiaroa, G.; Steinig, E.; Pasricha, S.; Williamson, D.

doi:10.1101/2024.05.14.593882

bioRxiv · 10.1101/2024.05.14.593882

PathoGD: an integrative genomics approach for CRISPR-based target design of rapid pathogen diagnostics

Low, S. J.·O'Neill, M.·Kerry, W. J.·Wild, N.·Krysiak, M.·Nong, Y.·Azzato, F.·Hor, E.·Williams, L.·Taiaroa, G.·Steinig, E.·Pasricha, S.·Williamson, D.

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Abstract

The design of highly specific primers and guide RNAs (gRNA) for CRISPR-based diagnostics is often a laborious process. Several tools exist for gRNA design, but most are tailored for genome editing applications. Here, we present PathoGD, an end-to-end bioinformatic pipeline comprising pangenome and k-mer modules for rapid and high-throughput design of primers and gRNAs for CRISPR-Cas12a-based pathogen detection. We validated and demonstrated high specificity of a subset of PathoGD-designed primers and gRNAs for the detection of Neisseria gonorrhoeae and Streptococcus pyogenes. PathoGD will serve as an important resource for designing CRISPR-based diagnostic assays for current and emerging pathogens.

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Low, S. J., O'Neill, M., Kerry, W. J., Wild, N., Krysiak, M., Nong, Y., Azzato, F., Hor, E., Williams, L., Taiaroa, G., Steinig, E., Pasricha, S., Williamson, D.. 2024-05-15. PathoGD: an integrative genomics approach for CRISPR-based target design of rapid pathogen diagnostics. https://doi.org/10.1101/2024.05.14.593882

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