CHANGE-seq-BE Detects Off-Target Effects of Base Editors

Researchers from St. Jude Children’s Research Hospital have developed a new method for assessing base editors. The technique, called Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing Base Editors (CHANGE-seq-BE), provides a sensitive, unbiased, and efficient way to detect off-target effects from CRISPR-based base editors. The work was published in Nature Biotechnology and offers scientists and clinicians a faster and more comprehensive understanding of how base editors operate across an entire genome.

Traditional CRISPR-Cas9 editing cuts DNA to make changes, but newer base editors modify individual DNA base pairs without cutting both strands, offering higher precision. Despite this improvement, detecting where these editors might unintentionally act has remained a significant technical and safety challenge. “We developed CHANGE-seq-BE to enable scientists to better understand base editors, an important class of CRISPR precise genome editors,” said senior author Shengdar Tsai. “It’s a simple and streamlined way to understand the global activity of base editors that enables researchers to select highly specific and active editor and target combinations for research or therapeutics.”

CHANGE-seq-BE has already supported clinical research, including an emergency request to the U.S. FDA to test a base editor targeting CD40L-deficient X-linked Hyper IgM (X-HIGM) syndrome, a rare immune disorder. In that case study, the technique confirmed 95.4% on-target activity and detected no significant off-target effects, providing key safety data for a patient’s treatment. “It was a really exciting application to support an emergency request to the FDA to treat a patient rapidly,” Tsai said. “It exemplifies how this method enables rapid understanding of what these editors are doing in the genome and helps advance promising active and specific therapeutics.”

The method’s design addresses long-standing trade-offs between sensitivity and efficiency. Many existing approaches either require comprehensive but expensive whole-genome sequencing or rely on biased pre-selected targets that may miss unanticipated edits. CHANGE-seq-BE combines both benefits by circularizing DNA fragments, exposing them to a base editor, and selecting only those circles showing edited sites for sequencing. This approach drastically reduces sequencing needs—about 5% of what competing methods require—while maintaining comprehensive coverage.

When compared with other methods, CHANGE-seq-BE detected nearly all identified off-targets plus additional ones missed elsewhere. Its sensitivity, cost-effectiveness, and flexibility have encouraged widespread adoption. Researchers in both clinical and basic science settings now use the technique to evaluate genome editing safety and identify optimal base editors early in development. “We’ve enabled those developing these therapies to quickly understand and find the base editors with the highest potential activity and specificity,” Tsai added. We hope that methods like CHANGE-seq-BE will open the door toward more genome editing therapies being developed for and reaching the patients who need them.”