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Detection of deleterious on-target effects after HDR-mediated CRISPR editing

By Isabel Weisheit, Joseph Kroeger, Rainer Malik, Julien Klimmt, Dennis Crusius, Angelika Dannert, Martin Dichgans, Dominik Paquet

Posted 29 Mar 2020
bioRxiv DOI: 10.1101/2020.03.27.012104 (published DOI: 10.1016/j.celrep.2020.107689)

CRISPR genome editing is a promising tool for translational research but can cause undesired editing outcomes, both on-target at the edited locus and off-target at other genomic loci. We investigated the occurrence of deleterious on-target effects in human stem cells after insertion of disease-related mutations by homology-directed repair (HDR). We identified large, mono-allelic genomic deletions and loss-of-heterozygosity that escaped standard quality controls in up to 40% of edited clones. To reliably detect such events, we developed simple, low-cost and universally applicable quantitative genotyping PCR (qgPCR) as well as sequencing-based tools and suggest their usage as additional quality controls after editing. This will help to ensure the integrity of edited loci and increase the reliability of CRISPR editing.

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