Work

Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications

Year: 2025

Type: article

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.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkaf389

Authors: Abyot Melkamu Mekonnen, Kang Seong, Hyeran Kim, Jeongbin Park

Institutions: Pusan National University, Kangwon National University

Language: English

Topic: CRISPR and Genetic Engineering

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funders: Rural Development Administration, National Research Foundation of Korea, Ministry of Science and ICT, South Korea