Efficient prioritization of CRISPR screen hits by accounting for targeting efficiency of guide RNA

Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343(6166):84–7.

Article  CAS  PubMed  Google Scholar 

Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, Miller BC, et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature. 2017;547(7664):413–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang D, Prager BC, Gimple RC, Aguilar B, Alizadeh D, Tang H, et al. CRISPR screening of CAR T cells and cancer stem cells reveals critical dependencies for cell-based therapies. Cancer Discov. 2021;11(5):1192–211.

Article  CAS  PubMed  Google Scholar 

Wang X, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, et al. In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. Cell. 2021;184(21):5357-74.e22.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong MB, Wang G, Chow RD, Ye L, Zhu L, Dai X, et al. Systematic immunotherapy target discovery using genome-scale in vivo CRISPR screens in CD8 T cells. Cell. 2019;178(5):1189-204.e23.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang HL, Hu BX, Li ZL, Du T, Shan JL, Ye ZP, et al. PKCβII phosphorylates ACSL4 to amplify lipid peroxidation to induce ferroptosis. Nat Cell Biol. 2022;24(1):88–98.

Article  CAS  PubMed  Google Scholar 

Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, et al. Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells. Science. 2018;361(6399):285–90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31(9):827–32.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim E, Hart T. Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier. Genome Medicine. 2021;13(1):2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liang S-Q, Liu P, Smith JL, Mintzer E, Maitland S, Dong X, et al. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Nat Commun. 2022;13(1):437.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, et al. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nat Commun. 2019;10(1):4063.

Article  PubMed  PubMed Central  Google Scholar 

Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, et al. The landscape of somatic copy-number alteration across human cancers. Nature. 2010;463(7283):899–905.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gonçalves E, Thomas M, Behan FM, Picco G, Pacini C, Allen F, et al. Minimal genome-wide human CRISPR-Cas9 library. Genome Biol. 2021;22(1):40.

Article  PubMed  PubMed Central  Google Scholar 

Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, et al. INDEL detection, the ‘Achilles heel’ of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res. 2020;48(21):11958–81.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016;34(2):184–91.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schmierer B, Botla SK, Zhang J, Turunen M, Kivioja T, Taipale J. CRISPR/Cas9 screening using unique molecular identifiers. Mol Syst Biol. 2017;13(10):945.

Article  PubMed  PubMed Central  Google Scholar 

Michlits G, Hubmann M, Wu S-H, Vainorius G, Budusan E, Zhuk S, et al. CRISPR-UMI: single-cell lineage tracing of pooled CRISPR–Cas9 screens. Nat Methods. 2017;14(12):1191–7.

Article  CAS  PubMed  Google Scholar 

Zhu S, Cao Z, Liu Z, He Y, Wang Y, Yuan P, et al. Guide RNAs with embedded barcodes boost CRISPR-pooled screens. Genome Biol. 2019;20(1):20.

Article  PubMed  PubMed Central  Google Scholar 

Diehl V, Wegner M, Grumati P, Husnjak K, Schaubeck S, Gubas A, et al. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic Acids Res. 2021;49(10):5684–704.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim E, Koo T, Park SW, Kim D, Kim K, Cho H-Y, et al. In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat Commun. 2017;8(1):14500.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018;556(7699):57–63.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee JK, Jeong E, Lee J, Jung M, Shin E, Kim Y-H, et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nature Commun. 2018;9(1):3048.

Article  Google Scholar 

Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science. 2016;351(6268):84–8.

Article  CAS  PubMed  Google Scholar 

Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017;49(12):1779–84.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Allen F, Behan F, Khodak A, Iorio F, Yusa K, Garnett M, et al. JACKS: joint analysis of CRISPR/Cas9 knockout screens. Genome Res. 2019;29(3):464–71.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, et al. In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat Methods. 2017;14(2):153–9.

Article  CAS  PubMed  Google Scholar 

Hegde M, Strand C, Hanna RE, Doench JG. Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens. PLoS ONE. 2018;13(5):e0197547.

Article  PubMed  PubMed Central  Google Scholar 

Mou H, Smith JL, Peng L, Yin H, Moore J, Zhang XO, et al. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biol. 2017;18(1):108.

Article  PubMed  PubMed Central  Google Scholar 

Aubrecht J, Goad ME, Schiestl RH. Tissue specific toxicities of the anticancer drug 6-thioguanine is dependent on the Hprt status in transgenic mice. J Pharmacol Exp Ther. 1997;282(2):1102–8.

CAS  PubMed  Google Scholar 

Liu M, Zhang W, Xin C, Yin J, Shang Y, Ai C, et al. Global detection of DNA repair outcomes induced by CRISPR-Cas9. Nucleic Acids Res. 2021;49(15):8732–42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Nat Med. 2018;24(7):927–30.

Article  CAS  PubMed  Google Scholar 

Sanson KR, Hanna RE, Hegde M, Donovan KF, Strand C, Sullender ME, et al. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nat Commun. 2018;9(1):5416.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finan C, Gaulton A, Kruger FA, Lumbers RT, Shah T, Engmann J, et al. The druggable genome and support for target identification and validation in drug development. Sci Transl Med. 2017;9(383):eaag1166.

Article  PubMed  PubMed Central  Google Scholar 

Perez AR, Pritykin Y, Vidigal JA, Chhangawala S, Zamparo L, Leslie CS, et al. GuideScan software for improved single and paired CRISPR guide RNA design. Nat Biotechnol. 2017;35(4):347–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

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