PrimeDesign software for rapid and simplified design of prime editing guide RNAs

Jonathan Y. Hsu, Julian Grünewald, Regan Szalay, Justine Shih, Andrew V. Anzalone, Kin Chung Lam, Max W. Shen, Karl Petri, David R. Liu, J. Keith Joung () and Luca Pinello ()
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Jonathan Y. Hsu: Department of Biological Engineering, Massachusetts Institute of Technology
Julian Grünewald: Molecular Pathology Unit, Massachusetts General Hospital
Regan Szalay: Molecular Pathology Unit, Massachusetts General Hospital
Justine Shih: Molecular Pathology Unit, Massachusetts General Hospital
Andrew V. Anzalone: Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT
Kin Chung Lam: Molecular Pathology Unit, Massachusetts General Hospital
Max W. Shen: Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT
Karl Petri: Molecular Pathology Unit, Massachusetts General Hospital
David R. Liu: Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT
J. Keith Joung: Molecular Pathology Unit, Massachusetts General Hospital
Luca Pinello: Molecular Pathology Unit, Massachusetts General Hospital

Nature Communications, 2021, vol. 12, issue 1, 1-6

Abstract: Abstract Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

Date: 2021
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DOI: 10.1038/s41467-021-21337-7

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