1. CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data
- Author
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Alona Levy-Jurgenson, Garrett R. Rettig, Ayal Hendel, Dor Breier, Matthew S. McNeill, Ido Amit, Zohar Yakhini, Ortal Iancu, Gavin Kurgan, Daniel Allen, Nimrod Ben Haim, Yu Wang, and Leon Anavy
- Subjects
CRISPR-Cas9 genome editing ,0301 basic medicine ,Bioinformatics ,Computer science ,Accurate estimation ,Science ,Software tool ,General Physics and Astronomy ,Computational biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Genome editing ,Humans ,CRISPR ,Statistical analysis ,Gene Editing ,Homeodomain Proteins ,Multidisciplinary ,Computational Biology ,Nuclear Proteins ,Medical practice ,Statistical model ,General Chemistry ,Human cell ,DNA-Binding Proteins ,Targeted gene repair ,HEK293 Cells ,030104 developmental biology ,CRISPR-Cas Systems ,Algorithms ,Software ,030217 neurology & neurosurgery ,Transcription Factors - Abstract
Controlling off-target editing activity is one of the central challenges in making CRISPR technology accurate and applicable in medical practice. Current algorithms for analyzing off-target activity do not provide statistical quantification, are not sufficiently sensitive in separating signal from noise in experiments with low editing rates, and do not address the detection of translocations. Here we present CRISPECTOR, a software tool that supports the detection and quantification of on- and off-target genome-editing activity from NGS data using paired treatment/control CRISPR experiments. In particular, CRISPECTOR facilitates the statistical analysis of NGS data from multiplex-PCR comparative experiments to detect and quantify adverse translocation events. We validate the observed results and show independent evidence of the occurrence of translocations in human cell lines, after genome editing. Our methodology is based on a statistical model comparison approach leading to better false-negative rates in sites with weak yet significant off-target activity., The control of off-target activity is a challenge for adapting CRISPR to therapeutic use. Here the authors present CRISPECTOR, a software tool to detect, evaluate and quantify editing activity, including translocations, from NGS data.
- Published
- 2021