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Genome editing technologies like CRISPR-Cas9 have transformed biology, medicine, and agriculture, but concerns remain about unintended edits at off-target DNA sites. These off-target effects can cause harmful mutations and are difficult to predict, as they depend not only on the guide RNA but also on an organism\u2019s unique genetic makeup. Most existing prediction tools rely on a standard reference genome, ignoring key variations like SNPs, insertions, and deletions that differ across individuals and alleles.<\/p>\n
To address this issue, researchers led by Professor Jeongbin Park from Pusan National University developed Variant-aware Cas-OFFinder, a web-based tool that improves off-target site prediction by accounting for individual genetic variation. Co-first authors Abyot Melkamu Mekonnen (PhD candidate) and Kang Seong (undergraduate at the time, now a master\u2019s student at KAIST), who conducted the study while at Pusan National University, said,\u00a0\u201cIt is very rewarding to know that the technology we developed can be of practical help in correcting individual genes.\u201d\u00a0The tool was tested using the human genome and pepper cultivars. Their findings were published online on 8 May, 2025 in the journal\u00a0Nucleic Acids Research<\/a>.<\/p>\n The Variant-aware Cas-OFFinder tool offers a significant step forward in personalized genome editing by incorporating genetic diversity directly into off-target predictions. It accepts phased single-sample VCF files and supports GPU acceleration, allowing application beyond standard model organisms. By reconstructing allele-specific genome sequences, the tool performs haplotype-level analysis, offering a detailed and accurate picture of potential off-target effects.<\/p>\n \u201cIn my view, genome editing tools should be as individualized as the genomes they target,\u201d\u00a0says Prof. Park.\u00a0\u201cOur tool lays the groundwork for more accurate and personalized editing strategies.\u201d<\/p>\n The team tested the tool on human and sweet pepper (Capsicum annuum) genomes using public and cultivar-specific sequencing data. In humans, it revealed off-target sites on chromosome 10 absent from the standard reference genome. In sweet pepper, it identified distinct allele-specific off-targets, useful for plant breeding.<\/p>\n Compared with existing tools like Cas-OFFinder and CRISPRitz, Variant-aware Cas-OFFinder consistently identified unique off-targets caused by small variants such as insertions and deletions. Although it does not yet detect large structural variants, it supports 557 species and 40 PAM types, and is fully customizable through YAML files.<\/p>\n \u201cPrecision genome editing requires precision tools,\u201d\u00a0remarks Prof. Park.\u00a0\u201cWe believe Variant-aware Cas-OFFinder will play a central role in developing safer, more effective CRISPR therapies and agricultural applications.\u201d<\/p>\n The tool is available both as a user-friendly web interface and a command-line version. Its source code, benchmark tools, and example datasets are freely available on GitHub and Zenodo. While its haplotype-level analysis can slow performance slightly compared to earlier tools, this trade-off enables greater accuracy and reliability in genome editing research.<\/p>\n Reference:\u00a0<\/b>Mekonnen AM, Seong K, Kim H, Park J. Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications. Nucleic Acids Res. 2025:gkaf389. doi:\u00a010.1093\/nar\/gkaf389<\/a><\/p>\n This article has been republished from the following materials<\/a>. Note: material may have been edited for length and content. For further information, please contact the cited source. Our press release publishing policy can be accessed here<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"
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