Scientists at St. Jude Children's Research Hospital have introduced a new method called CHANGE-seq-BE to improve the assessment of precision genome editing technologies. The approach is designed to identify small off-target sites created by gene editing tools, which are a safety concern and difficult to detect using existing techniques.
Traditional CRISPR-Cas9 technology edits genes by cutting DNA, but newer methods like base editors can change individual DNA base pairs with more precision. However, ensuring these editors do not make unintended changes elsewhere in the genome remains a challenge.
The new method, Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing Base Editors (CHANGE-seq-BE), allows researchers to comprehensively and efficiently find off-target edits without bias. According to St. Jude scientists, it requires fewer resources than current approaches and has already been used in clinical contexts.
In a recent case study described in Nature Biotechnology, CHANGE-seq-BE was applied during an emergency request to the Food and Drug Administration (FDA) for treating CD40L-deficient X-linked Hyper IgM (X-HIGM) syndrome with a base editor. The tool confirmed that 95.4% of editing occurred at the intended site with no significant off-target effects, providing important safety data for advancing patient treatment.
"It was a really exciting application to support an emergency request to the FDA to treat a patient rapidly," said Tsai, one of the researchers involved in developing CHANGE-seq-BE. "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."
Tsai's team developed this approach because conventional methods require either extensive whole genome sequencing or rely on pre-selected targets—each presenting limitations in cost or scope. CHANGE-seq-BE starts with dividing the genome into circular segments before exposing them to base editors; only those segments where editing occurs are then sequenced, reducing overall resource use.
"When we directly compared it to other methods, CHANGE-seq-BE found almost all sites nominated by those methods, as well as many that it was exclusively able to detect," Tsai said. "We showed that this unbiased approach was more sensitive while using only about 5% of the sequencing reads."
The technique has been made available through published experimental protocols and software so other research groups can adopt it easily. It is already being integrated into clinical trial planning at St. Jude and other institutions as both a safety and efficiency evaluation tool for genome editing treatments.
"We've enabled those developing these therapies to quickly understand and find the base editors with the highest potential activity and specificity," Tsai said. "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."
