PT  - JOURNAL ARTICLE
AU  - Helen Lindsay
AU  - Alexa Burger
AU  - Berthin Biyong
AU  - Anastasia Felker
AU  - Christopher Hess
AU  - Elena Chiavacci
AU  - Jonas Zaugg
AU  - Carolin Anders
AU  - Martin Jinek
AU  - Christian Mosimann
AU  - Mark D. Robinson
TI  - CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments
AID  - 10.1101/034140
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 034140
4099  - http://biorxiv.org/content/early/2016/03/10/034140.short
4100  - http://biorxiv.org/content/early/2016/03/10/034140.full
AB  - 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.