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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Bibliographic Details
Published in:BMC genomics Vol. 26; no. 1; pp. 198 - 9
Main Authors: Lukasiak, Sebastian, Kalinka, Alex, Gupta, Nikhil, Papadopoulos, Angelos, Saeed, Khalid, McDermott, Ultan, Hannon, Gregory James, Ross-Thriepland, Douglas, Walter, David
Format: Journal Article
Language:English
Published: London BioMed Central 26.02.2025
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
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 Access:Get full text
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Summary: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.
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ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-025-11386-3