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

  • Nat Commun. 2021 Feb 15;12(1):1034. doi: 10.1038/s41467-021-21337-7.
Jonathan Y Hsu  1  2  3 ,  Julian Grünewald  2  3  4 ,  Regan Szalay  2  3 ,  Justine Shih  2  3 ,  Andrew V Anzalone  5  6  7 ,  Kin Chung Lam  2  3  4 ,  Max W Shen  5  6  7  8 ,  Karl Petri  2  3  4 ,  David R Liu  5  6  7 ,  J Keith Joung  9  10  11 ,  Luca Pinello  12  13  14
Affiliations
  • 1. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • 2. Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.
  • 3. Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.
  • 4. Department of Pathology, Harvard Medical School, Boston, MA, USA.
  • 5. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • 6. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
  • 7. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
  • 8. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • 9. Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA. [email protected].
  • 10. Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA. [email protected].
  • 11. Department of Pathology, Harvard Medical School, Boston, MA, USA. [email protected].
  • 12. Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA. [email protected].
  • 13. Department of Pathology, Harvard Medical School, Boston, MA, USA. [email protected].
  • 14. Broad Institute of Harvard and MIT, Cambridge, MA, USA. [email protected].
PMID: 33589617 DOI: 10.1038/s41467-021-21337-7
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.