Minimal genome-wide human CRISPR-Cas9 library

被引:36
|
作者
Goncalves, Emanuel [1 ]
Thomas, Mark [1 ]
Behan, Fiona M. [1 ]
Picco, Gabriele [1 ]
Pacini, Clare [1 ,2 ]
Allen, Felicity [1 ]
Vinceti, Alessandro [3 ]
Sharma, Mamta [1 ]
Jackson, David A. [1 ]
Price, Stacey [1 ]
Beaver, Charlotte M. [1 ]
Dovey, Oliver [1 ]
Parry-Smith, David [1 ]
Iorio, Francesco [1 ,3 ]
Parts, Leopold [1 ,4 ]
Yusa, Kosuke [5 ]
Garnett, Mathew J. [1 ]
机构
[1] Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton, England
[2] Open Targets, Wellcome Genome Campus, Cambridge CB10 1SA, England
[3] Human Technopole, Via Cristina Belgioioso 147, I-20157 Milan, Italy
[4] Univ Tartu, Dept Comp Sci, 18 Narva St, Tartu, Estonia
[5] Kyoto Univ, Inst Frontier Life & Med Sci, Kyoto 6068507, Japan
基金
英国惠康基金;
关键词
CRISPR-Cas9; Genome-wide; Minimal library; Organoid; KS score; GENETIC SCREENS; DRUG-SENSITIVITY; POOLED LIBRARY; KNOCKOUT; DESIGN; VULNERABILITIES; IDENTIFICATION; SPECIFICITY; DISCOVERY; TARGETS;
D O I
10.1186/s13059-021-02268-4
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.
引用
收藏
页数:14
相关论文
共 50 条
  • [21] Genome-wide CRISPR-Cas9 screens identify mechanisms of BET bromodomain inhibitor sensitivity
    Estoppey, David
    Schutzius, Gabi
    Kolter, Christian
    Salathe, Adrian
    Wunderlin, Tiffany
    Meyer, Amandine
    Nigsch, Florian
    Bouwmeester, Tewis
    Hoepfner, Dominic
    Kirkland, Susan
    ISCIENCE, 2021, 24 (11)
  • [22] Genome-Wide Off-Target Analysis in CRISPR-Cas9 Modified Mice and Their Offspring
    Dong, Yan
    Li, Haimei
    Zhao, Liang
    Koopman, Peter
    Zhang, Feng
    Huang, Johnny X.
    G3-GENES GENOMES GENETICS, 2019, 9 (11): : 3645 - 3651
  • [23] The genomic landscape of sensitivity to arsenic trioxide uncovered by genome-wide CRISPR-Cas9 screening
    Chen, Jun-Zhu
    Wang, Li-Na
    Luo, Xue-Qun
    Tang, Yan-Lai
    FRONTIERS IN ONCOLOGY, 2023, 13
  • [24] Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes
    Jeremy Vicencio
    Carlos Sánchez-Bolaños
    Ismael Moreno-Sánchez
    David Brena
    Charles E. Vejnar
    Dmytro Kukhtar
    Miguel Ruiz-López
    Mariona Cots-Ponjoan
    Alejandro Rubio
    Natalia Rodrigo Melero
    Jesús Crespo-Cuadrado
    Carlo Carolis
    Antonio J. Pérez-Pulido
    Antonio J. Giráldez
    Benjamin P. Kleinstiver
    Julián Cerón
    Miguel A. Moreno-Mateos
    Nature Communications, 13
  • [25] Identifying mechanisms of acquired resistance to lorlatinib utilizing a genome-wide CRISPR-Cas9 screen
    Kalna, Joshua Renn
    Matkar, Smita
    O'Drisoll, Emily
    Balyasny, Skye
    Calafatti, Matteo
    Gerelus, Mark
    Groff, Dave
    Acholla, Tina
    Casey, Colleen E.
    Kamitsuka, Paul
    Li, Grant
    Pastor, Steven J.
    Witek, Gabriela
    Krytska, Kateryna
    Lindsay, Jarrett
    Shalem, Ophir
    Mosse, Yael P.
    CANCER RESEARCH, 2024, 84 (06)
  • [26] Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes
    Vicencio, Jeremy
    Sanchez-Bolanos, Carlos
    Moreno-Sanchez, Ismael
    Brena, David
    Vejnar, Charles E.
    Kukhtar, Dmytro
    Ruiz-Lopez, Miguel
    Cots-Ponjoan, Mariona
    Rubio, Alejandro
    Rodrigo Melero, Natalia
    Crespo-Cuadrado, Jesus
    Carolis, Carlo
    Perez-Pulido, Antonio J.
    Giraldez, Antonio J.
    Kleinstiver, Benjamin P.
    Ceron, Julian
    Moreno-Mateos, Miguel A.
    NATURE COMMUNICATIONS, 2022, 13 (01)
  • [27] Genome-wide CRISPR-Cas9 screen for the identification of genes modulating lenvatinib resistance in HCC
    Zhou, Shuang
    Abe, Yuichi
    Kajino, Taisuke
    Isomura, Hisanori
    Tanaka, Miyako
    Yamaguchi, Rui
    Suganami, Takayoshi
    Taguchi, Ayumu
    CANCER SCIENCE, 2025, 116 : 1363 - 1363
  • [28] Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy
    Lek, Angela
    Zhang, Yuanfan
    Woodman, Keryn G.
    Huang, Shushu
    DeSimone, Alec M.
    Cohen, Justin
    Ho, Vincent
    Conner, James
    Mead, Lillian
    Kodani, Andrew
    Pakula, Anna
    Sanjana, Neville
    King, Oliver D.
    Jones, Peter L.
    Wagner, Kathryn R.
    Lek, Monkol
    Kunkel, Louis M.
    SCIENCE TRANSLATIONAL MEDICINE, 2020, 12 (536)
  • [29] Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells
    Kim, Daesik
    Bae, Sangsu
    Park, Jeongbin
    Kim, Eunji
    Kim, Seokjoong
    Yu, Hye Ryeong
    Hwang, Jinha
    Kim, Jong-Il
    Kim, Jin-Soo
    NATURE METHODS, 2015, 12 (03) : 237 - +
  • [30] Genome-wide CRISPR-Cas9 screens reveal candidate therapeutic targets and tumor suppressor genes for human glioma
    Ding, Yu
    Toledo, Chad
    Hoellerbauer, Pia
    Basom, Ryan
    Girad, Emily
    Lee, Eunjee
    Corrin, Philip
    Lin, Qi
    Li, Xiao-Nan
    Nam, Do-Hyun
    Lee, Jeongwu
    Zhu, Jun
    Pollard, Steven
    Delrow, Jeffery
    Olson, Jim
    Paddison, Patrick J.
    CANCER RESEARCH, 2015, 75