Scientists and clinicians can more accurately evaluate precision genome-editing technologies using a newly developed method reported today by St. Jude Children’s Research Hospital. A major focus of improving CRISPR-based gene editing has been identifying rare off-target edits that pose potential safety risks—an effort that is both technically challenging and resource-intensive. To address this limitation, St. Jude researchers developed Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing for Base Editors (CHANGE-seq-BE), an unbiased, sensitive, and resource-efficient approach for detecting off-target base editing events. The method outperformed existing techniques and has already supported clinical research. The findings were published in Nature Biotechnology.
Traditional CRISPR-Cas9 genome editing relies on cutting DNA, but newer precision tools, such as base editors, enable targeted conversion of individual DNA base pairs without introducing double-strand breaks. CHANGE-seq-BE was designed specifically to characterize the genome-wide activity of these precision editors.
“We developed CHANGE-seq-BE to allow researchers to better understand base editors, an important class of precise genome-editing tools,” said Shengdar Tsai, PhD, corresponding author and investigator in the St. Jude Department of Hematology. “This streamlined approach provides a comprehensive view of base editor activity, enabling the selection of highly specific and effective editor–target combinations for research and therapeutic use.”
The method has already been applied in clinical research settings. The study includes a case involving an emergency FDA application for a base editing therapy targeting CD40L-deficient X-linked Hyper IgM syndrome (X-HIGM), a rare genetic immune disorder. CHANGE-seq-BE demonstrated 95.4% on-target specificity with no detectable significant off-target activity, providing critical safety data to support clinical decision-making.
CHANGE-seq-BE combines comprehensive genome-wide coverage with efficient resource utilization. Unlike whole-genome sequencing approaches, which are costly and time-consuming, or biased methods that preselect potential off-target sites, CHANGE-seq-BE enables unbiased detection while requiring only a fraction of sequencing reads. In direct comparisons, the method identified nearly all off-target sites found by existing techniques, as well as additional sites uniquely detected by CHANGE-seq-BE, using approximately 5% of the sequencing depth.
