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bioRxiv · 10.64898/2026.06.13.732078

Genome-wide structural variant landscape following HDR-enhanced CRISPR editing in human hematopoietic stem and progenitor cells

Cloarec-Ung, F.·Sauvageau, G.·Sheppard, H.·Lansdorp, P.·Knapp, D.
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Abstract

DNA-PK inhibitors (DNA-PKi) have emerged as potent enhancers of homology-directed repair (HDR) in genome editing, however, recent studies have reported that such inhibitors can induce large-scale structural variations (SVs) raising safety concerns. To investigate factors influencing SV induction in human hematopoietic stem and progenitor cells (HSPCs), we employed a combination of on-target long-read nanopore sequencing and unbiased genome wide detection of SVs using Strand-seq. Our results show that editing alone results in a high frequency of large on-target deletions which were modestly increased by DNA-PK inhibition and could be mitigated using DNA polQ inhibitors. Genome-wide SVs were also induced at low frequencies by editing but were not substantially increased with DNA-PKi. SVs including translocations were, however, increased with multiple simultaneous editing. Our results highlight that edit-induced SVs are not limited to DNA-PKi enhanced protocols, thus careful assessment will be critical to ensure the safety of any edited therapeutic cell product.

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Cloarec-Ung, F., Sauvageau, G., Sheppard, H., Lansdorp, P., Knapp, D.. 2026-06-15. Genome-wide structural variant landscape following HDR-enhanced CRISPR editing in human hematopoietic stem and progenitor cells. https://doi.org/10.64898/2026.06.13.732078

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