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CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments

By Helen Lindsay, Alexa Burger, Berthin Biyong, Anastasia Felker, Christopher Hess, Elena Chiavacci, Jonas Zaugg, Carolin Anders, Martin Jinek, Christian Mosimann, Mark D Robinson

Posted 10 Dec 2015
bioRxiv DOI: 10.1101/034140 (published DOI: 10.1038/nbt.3628)

CRISPR-Cas9 and related technologies efficiently alter genomic DNA at targeted positions and have far-reaching implications for functional screening and therapeutic gene editing. Understanding and unlocking this potential requires accurate evaluation of editing efficiency. We show that methodological decisions for analyzing sequencing data can significantly affect mutagenesis efficiency estimates and we provide a comprehensive R-based toolkit, CrispRVariants and accompanying web tool CrispRVariantsLite, that resolves and localizes individual mutant alleles with respect to the endonuclease cut site. CrispRVariants-enabled analyses of newly generated and existing genome editing datasets underscore how careful consideration of the full variant spectrum gives insight toward effective guide and amplicon design as well as the mutagenic process.

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