Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

Nat Commun. 2021 May 28;12(1):3238. doi: 10.1038/s41467-021-23576-0.


The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, we train a deep learning model, CRISPRon, on 23,902 gRNAs. Compared to existing tools, CRISPRon exhibits significantly higher prediction performances on four test datasets not overlapping with training data used for the development of these tools. Furthermore, we present an interactive gRNA design webserver based on the CRISPRon standalone software, both available via https://rth.dk/resources/crispr/ . CRISPRon advances CRISPR applications by providing more accurate gRNA efficiency predictions than the existing tools.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Cas Systems / genetics
  • Computational Biology / methods*
  • Deep Learning*
  • Gene Editing*
  • Genetic Vectors / genetics
  • HEK293 Cells
  • Humans
  • Lentivirus / genetics
  • Plasmids / genetics
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • Software


  • RNA, Guide, CRISPR-Cas Systems