Journal
GENETICS
Volume 212, Issue 2, Pages 377-385Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.119.302089
Keywords
CRISPR; base editing; gene editing; genome; wide mutagenesis; gRNA design
Categories
Funding
- Canadian Institutes of Health Research [299432, 324265, 387697, 364920, 384483]
- Japan Society for the Promotion of Science [S15734, S17161]
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CRISPR-mediated base editors have opened unique avenues for scar-free genome-wide mutagenesis. Here, we describe a comprehensive computational workflow called beditor that can be broadly adapted for designing guide RNA libraries with a range of CRISPR-mediated base editors, Protospacer Adjacent Motif (PAM) recognition sequences, and genomes of many species. Additionally, to assist users in selecting the best sets of guide RNAs for their experiments, a priori estimates of editing efficiency, called beditor scores, are calculated. These beditor scores are intended to select guide RNAs that conform to requirements for optimal base editing: the editable base falls within maximum activity window of the CRISPR-mediated base editor and produces nonconfounding mutational effects with minimal predicted off-target effects. We demonstrate the utility of the software by designing guide RNAs for base editing to model or correct thousands of clinically important human disease mutations.
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