RT Journal Article SR Electronic T1 Detection of deleterious on-target effects after HDR-mediated CRISPR editing JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.03.27.012104 DO 10.1101/2020.03.27.012104 A1 Isabel Weisheit A1 Joseph Kroeger A1 Rainer Malik A1 Julien Klimmt A1 Dennis Crusius A1 Angelika Dannert A1 Martin Dichgans A1 Dominik Paquet YR 2020 UL http://biorxiv.org/content/early/2020/03/29/2020.03.27.012104.abstract AB 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.