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Nucleic Acids Res., May 08 2025, gkaf389 | https://doi.org/10.1093/nar/gkaf389
Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications
Abyot Melkamu Mekonnen1,†, Kang Seong2,3,†, Hyeran Kim4, Jeongbin Park1,2,*
1Department of Information Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
2School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
3Present address: Kang Seong, School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34051, Republic of Korea
4Department of Biological Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
*To whom correspondence should be addressed. : Jeongbin Park
†The first two authors should be regarded as Joint First Authors.
1Department of Information Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
2School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
3Present address: Kang Seong, School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34051, Republic of Korea
4Department of Biological Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
*To whom correspondence should be addressed. : Jeongbin Park
†The first two authors should be regarded as Joint First Authors.
Abstract
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.
논문정보
- Research article
- 2025년 05월 (BRIC 등록일 2025-05-09)
- 국내 연구진
- 생명과학 > 생물공학
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