Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 Journal Article

   


Authors: Schmidt, H.; Zhang, M.; Chakarov, D.; Bansal, V.; Mourelatos, H.; Sánchez-Rivera, F. J.; Lowe, S. W.; Ventura, A.; Leslie, C. S.; Pritykin, Y.
Article Title: Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
Abstract: 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. © The Author(s) 2025.
Keywords: controlled study; unclassified drug; human cell; genetics; nonhuman; polymerase chain reaction; animal cell; mouse; animal; animals; mice; diagnostic procedure; interleukin 2; gene expression; rna interference; gamma interferon; algorithm; genomics; genome; dna sequence; doxycycline; software; dna isolation; procedures; guide rna; human; article; long untranslated rna; crispr; crispr associated protein; clustered regularly interspaced short palindromic repeat; crispr cas system; burrows-wheeler transform; gene editing; crispr-cas systems; crispr-cas9 system; a-549 cell line; clustered regularly interspaced short palindromic repeats; crispr associated endonuclease cas9; rna, guide, crispr-cas systems; crispr-cas system guide rna; guidescan2; off-targets; web interface; crispr associated endonuclease cas12a; cell line by cell type; kbm-7 cell line; product design; specificity analysis; v6.5 mouse embryonic stem cells
Journal Title: Genome Biology
Volume: 26
ISSN: 1465-6906
Publisher: Biomed Central Ltd  
Date Published: 2025-02-26
Start Page: 41
Language: English
DOI: 10.1186/s13059-025-03488-8
PUBMED: 40011959
PROVIDER: scopus
PMCID: PMC11863968
DOI/URL:

https://www.scopus.com/inward/record.uri?eid=2-s2.0-85219506538&doi=10.1186%2fs13059-025-03488-8&partnerID=40&md5=fda6a89bed88e97643318fdbe7a9b28c
Notes: Source: Scopus
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MSK Authors
  1. Andrea Ventura
    56 Ventura
  2. Christina Leslie
    187 Leslie
  3. Scott W Lowe
    249 Lowe
  4. Yury Pritykin
    18 Pritykin
  5. Minsi Zhang
    18 Zhang
  6. Francisco Sanchez-Rivera
    29 Sanchez-Rivera
  7. Henri C Schmidt
    3 Schmidt
  8. Haralambos Mourelatos
    1 Mourelatos
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