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; Luca Pinello

doi:10.1038/s41467-021-21337-7

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, Luca Pinello

Research output: Contribution to journal › Article › peer-review

115 Scopus citations

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.

Original language	English
Article number	1034
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-21337-7
State	Published - 1 Dec 2021
Externally published	Yes

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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.",

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AU - Szalay, Regan

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AU - Anzalone, Andrew V.

AU - Lam, Kin Chung

AU - Shen, Max W.

AU - Petri, Karl

AU - Liu, David R.

AU - Keith Joung, J.

AU - Pinello, Luca

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

Abstract

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