Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.
Authors
- Henri Schmidt (ORCID: https://orcid.org/0000-0002-0132-3472)
- Vineet Bansal (ORCID: https://orcid.org/0009-0006-7311-5345)
- Minsi Zhang (ORCID: https://orcid.org/0009-0003-6182-1195)
- Scott W. Lowe (ORCID: https://orcid.org/0000-0002-5284-9650)
- Francisco J. Sánchez‐Rivera (ORCID: https://orcid.org/0000-0002-8466-8563)
- Andrea Ventura (ORCID: https://orcid.org/0000-0003-4320-9907)
- Yuri Pritykin
- Christina S. Leslie (ORCID: https://orcid.org/0000-0002-4571-5910)
- Haralambos Mourelatos
- Dimitar Chakarov
Institutions
- Memorial Sloan Kettering Cancer Center (US)
- Princeton University (US)
- Cornell University (US)
- Tri-Institutional PhD Program in Chemical Biology (US)
- Massachusetts Institute of Technology (US)
Publication Details
- Journal
- Genome biology
- Published
- 2025-02-26
- DOI
- https://doi.org/10.1186/s13059-025-03488-8
- Citations
- 14
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 10.48
Funders
- Howard Hughes Medical Institute
- Ludwig Institute for Cancer Research
- National Institutes of Health