A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency

Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-t...

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Veröffentlicht in:	BMC genomics Jg. 26; H. 1; S. 198 - 9
Hauptverfasser:	Lukasiak, Sebastian, Kalinka, Alex, Gupta, Nikhil, Papadopoulos, Angelos, Saeed, Khalid, McDermott, Ultan, Hannon, Gregory James, Ross-Thriepland, Douglas, Walter, David
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London BioMed Central 26.02.2025 BioMed Central Ltd Springer Nature B.V BMC
Schlagworte:	Algorithms Analysis Animal Genetics and Genomics Anopheles Benchmarking Benchmarks Biomedical and Life Sciences Comparative analysis CRISPR CRISPR-Cas Systems CRISPR-Cas9 Efficiency Gene Editing - methods Gene Library Genes Genome-wide Genomes Genomic libraries Genomics Health aspects Humans Life Sciences Methods Microarrays Microbial Genetics and Genomics Plant Genetics and Genomics Pooled CRISPR screening Proteomics RNA RNA, Guide, CRISPR-Cas Systems - genetics SgRNA selection algorithm Austria SgRNA selection algorithm Pooled CRISPR screening Genome-wide CRISPR-Cas9
ISSN:	1471-2164, 1471-2164
Online-Zugang:	Volltext
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Zusammenfassung:	Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale.
Bibliographie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1471-2164 1471-2164
DOI:	10.1186/s12864-025-11386-3