Mekonnen Abyot Melkamu, Seong Kang, Kim Hyeran, Park Jeongbin
Department of Information Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea.
School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea.
Nucleic Acids Res. 2025 Jul 7;53(W1):W118-W124. doi: 10.1093/nar/gkaf389.
Genome editing based on CRISPR systems has been widely used in the vast areas of biomedical and agricultural applications. However, identifying the potential off-target sites remains challenging, particularly in individuals with diverse genetic variations. Several in silico tools have been developed to predict potential off-target sites, but they have limitations on their performance and scalability. In this paper, we present "Variant-aware Cas-OFFinder," a novel pipeline based on Cas-OFFinder for identifying potential off-target sites by accounting for individual genetic variants. We benchmarked the pipeline's improved scalability and performance with the human genome and pepper cultivars, having unique potential off-target sites on each allele at the haplotype level. The web tool is open to all users without a login requirement and is freely available online at https://rgetoolkit.com/var-cas-offinder.
基于CRISPR系统的基因组编辑已广泛应用于生物医学和农业等众多领域。然而，识别潜在的脱靶位点仍然具有挑战性，尤其是在具有不同遗传变异的个体中。已经开发了几种计算机工具来预测潜在的脱靶位点，但它们在性能和可扩展性方面存在局限性。在本文中，我们提出了“变异感知Cas-OFFinder”，这是一种基于Cas-OFFinder的新型流程，通过考虑个体遗传变异来识别潜在的脱靶位点。我们用人类基因组和辣椒品种对该流程的改进后的可扩展性和性能进行了基准测试，这些品种在单倍型水平的每个等位基因上都有独特的潜在脱靶位点。该网络工具向所有用户开放，无需登录，可在https://rgetoolkit.com/var-cas-offinder上免费在线获取。
