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Minimal genome-wide human CRISPR-Cas9 library

Emanuel Gonçalves, Mark Thomas, Fiona M. Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Alessandro Vinceti, Mamta Sharma, David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey (+5 others)
2021 Genome Biology  
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.  ...  Acknowledgements We acknowledge Joel Rein for helpful comments on the integration of WGE annotations.  ... 
doi:10.1186/s13059-021-02268-4 pmid:33478580 pmcid:PMC7818936 fatcat:xquw27ddhfhn7kc3vbyh76rr6u

GUIDES: sgRNA design for loss-of-function screens [article]

Joshua A. Meier, Feng Zhang, Neville Sanjana
2017 bioRxiv   pre-print
GUIDES combines multi-tissue RNA-sequencing data to target expressed exons, protein annotation to target functional domains, sophisticated on-target and off-target guide RNA scoring and other optimizations  ...  GUIDES (Graphical User Interface for DNA Editing Screens) is a web-based tool for the design of custom, large-scale CRISPR libraries for loss-of-function screens in human and mouse.  ...  Other CRISPR library design tools have also used on-target efficiency scoring to help automate sgRNA design, but do not include RNA expression or protein domain identification to sgRNA targeting 8 ( Table  ... 
doi:10.1101/168849 fatcat:upwnmvrljfacbmrtxfjpkjsmje

C-RNNCrispr: prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks

Guishan Zhang, Zhiming Dai, Xianhua Dai
2020 Computational and Structural Biotechnology Journal  
In this study, we proposed C-RNNCrispr, a hybrid convolutional neural networks (CNNs) and bidirectional gate recurrent unit network (BGRU) framework, to predict CRISPR/Cas9 sgRNA on-target activity.  ...  CRISPR/Cas9 is a hot genomic editing tool, but its success is limited by the widely varying target efficiencies among different single guide RNAs (sgRNAs).  ...  Inspired by these studies, we proposed a unified CNN-RNN framework to predict CRISPR/Cas9 sgRNA on-target activity.  ... 
doi:10.1016/j.csbj.2020.01.013 pmid:32123556 pmcid:PMC7037582 fatcat:7ldpr5e7bbelpf7y5snbfbfi3q

sgRNA-PSM: predict sgRNAs on-target activity based on Position Specific Mismatch

Bin Liu, Zhihua Luo, Juan He
2020 Molecular Therapy: Nucleic Acids  
As a key technique for the CRISPR-Cas9 system, identification of single-guide RNAs (sgRNAs) on-target activity is critical for both theoretical research (investigation of RNA functions) and real-world  ...  Because of its importance, several computational predictors have been proposed to predict sgRNAs on-target activity.  ...  Rational design of sgRNA is a crucial part for CRISPR-Cas9. Therefore, the prediction of sgRNAs on-target activity is very important for CRISPR-Cas9.  ... 
doi:10.1016/j.omtn.2020.01.029 pmid:32199128 pmcid:PMC7083770 fatcat:zvtzjycekva7zcruimi63u5uea

Minimal genome-wide human CRISPR-Cas9 library [article]

Emanuel Gonçalves, Mark Thomas, Fiona M Behan, Gabriele Picco, Clare Pacini, Felicity Allen, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa, Mathew J Garnett
2019 bioRxiv   pre-print
We designed a minimal genome-wide human CRISPR-Cas9 library (MinLibCas9), optimised by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 46% reduction in size compared  ...  MinLibCas9 improves the efficiency of CRISPR-Cas9 loss-of-function screens and expands their application to complex models and assays.  ...  Acknowledgements We acknowledge Joel Rein for helpful comments on the integration of WGE annotations. We would also like to thank the core support provided by the Cellular  ... 
doi:10.1101/848895 fatcat:3ptos46jbnexdfqrkeqc2oavhy

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives

Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu
2019 Genome Research  
Various methods have been developed to lessen this requirement, but there are still three tasks for accurate CRISPR screen analysis that involve bioinformatic know-how, if not prowess: designing a proper  ...  To make CRISPR screen analysis more reliable as well as more readily accessible, we have developed a new algorithm, called CRISPRBetaBinomial or CB2 Based on the beta-binomial distribution, which is better  ...  In the first CRISPR screen on an RT112 cell line, we expected to see the depletion of sgRNAs targeting RPL5 in group T 1 .  ... 
doi:10.1101/gr.245571.118 pmid:31015259 pmcid:PMC6581060 fatcat:crd7iinc7bg3pfyewua6ew7d6a

GUIDES: sgRNA design for loss-of-function screens

Joshua A Meier, Feng Zhang, Neville E Sanjana
2017 Nature Methods  
Other CRISPR library design tools have also used on-target efficiency scoring to help automate sgRNA design, but do not include RNA expression or protein domain identification to sgRNA targeting 8 ( Table  ...  When targeting the same sets of genes, sgRNAs designed with this criterion have a ~30% higher on-target efficiency score (Supplementary Fig. 3) .  ... 
doi:10.1038/nmeth.4423 pmid:28858339 pmcid:PMC5870754 fatcat:a7ok56hkurfprbegphmrsmk7uy

CRISPRCloud2: A cloud-based platform for deconvoluting CRISPR screen data [article]

Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu
2018 bioRxiv   pre-print
information across multiple sgRNAs targeting the same gene, a user-friendly data visualization and query interface, as well as easy linking to other CRISPR tools and bioinformatics resources for target  ...  CRISPRCloud2 is a one-stop shop for labs analyzing CRISPR screen data.  ...  target hits based on summary statistics.  ... 
doi:10.1101/309302 fatcat:kvz4j4dsb5d67olafpfaaggbci

Computational approaches for effective CRISPR guide RNA design and evaluation

Guanqing Liu, Yong Zhang, Tao Zhang
2019 Computational and Structural Biotechnology Journal  
Successful editing by CRISPR requires an appropriate Cas protein and guide RNA. However, low cleavage efficiency and off-target effects hamper the development and application of CRISPR/Cas systems.  ...  The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/ CRISPR-associated (Cas) system has emerged as the main technology for gene editing.  ...  The Church laboratory developed software called sgRNA scorer to calculate sgRNA on-target scores based on their SVM model [14] .  ... 
doi:10.1016/j.csbj.2019.11.006 pmid:31890142 pmcid:PMC6921152 fatcat:3wm675m6qzdsdnkql74zxmgxbe

Computational Tools and Resources for CRISPR/Cas 9 Genome Editing Method

Vijay Kumar Garlapati
2017 MOJ Proteomics & Bioinformatics  
To aid the researchers in designing the optimal sequences for CRISPR/Cas9 experiments, a multitude of bioinformatics tools and resources have been developed and are currently used.  ...  We hope that such a compilation will enable researchers to select the resources based on functionality, ease of use, availability, and specific research needs.  ...  With the availability of multiple resources for sgRNA design, the prediction accuracy and validated benchmark sets are utmost important for efficient targeted genome editing research. 16 . 16 Grissa I  ... 
doi:10.15406/mojpb.2017.05.00164 fatcat:wcfy6xi5w5ctzgdjlc7puaiare

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia Ponomarenko, Roderic Guigo, Rory Johnson, Ilya Ioshikhes
2017 PLoS Computational Biology  
We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model.  ...  CRISPR-Cas9 requires researchers to design small RNA molecules called sgRNAs to target their region of interest. A large number of bioinformatic tools exist for this task.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1371/journal.pcbi.1005341 pmid:28253259 pmcid:PMC5333799 fatcat:mkhsk7sponcq7hrbtwwnenta6u

Pooled CRISPR screening at high sensitivity with an empirically designed sgRNA library [article]

Luisa Henkel, Benedikt Rauscher, Barbara Schmitt, Jan Winter, Michael Boutros
2020 bioRxiv   pre-print
We further systematically analyzed published CRISPR screens in human cells to identify single-guide (sg)RNAs with consistent high on-target and low off-target activity.  ...  Given their broad utility in functionally annotating genomes, the experimental design of genome-scale CRISPR screens can vary greatly and criteria for optimal experimental implementation and library composition  ...  We further aimed to benchmark sgRNAs selected for the HD CRISPR Library based on commonly used sgRNA design scores.  ... 
doi:10.1101/2020.04.25.061135 fatcat:lqgkqtuoizayhdzaezs2sef2ie

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

Luisa Henkel, Benedikt Rauscher, Barbara Schmitt, Jan Winter, Michael Boutros
2020 BMC Biology  
We further systematically analyzed published CRISPR screens in human cells to identify single-guide (sg) RNAs with consistent high on-target and low off-target activity.  ...  Given their broad utility in functionally annotating genomes, the application and interpretation of genome-scale CRISPR screens would greatly benefit from consistent and optimal design criteria.  ...  Published CRISPR screening datasets used for the design of the HD CRISPR library were derived from GenomeCRISPR (http://genomecrispr.org) [25] .  ... 
doi:10.1186/s12915-020-00905-1 pmid:33228647 fatcat:abjcifxu3bg2rkpzqiduk6b72m

CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci

Krzysztof Chylinski, Maria Hubmann, Ruth E. Hanna, Connor Yanchus, Georg Michlits, Esther C. H. Uijttewaal, John Doench, Daniel Schramek, Ulrich Elling
2019 Nature Communications  
Thus, CRISPR-Switch substantially increases the versatility of gene editing through precise and rapid switching ON or OFF sgRNA activity, as well as switching OVER to secondary sgRNAs.  ...  Switch-ON facilitates controlled, rapid induction of sgRNA activity.  ...  Benchmarking of CRISPR-Switch to alternative systems.  ... 
doi:10.1038/s41467-019-13403-y pmid:31784531 pmcid:PMC6884486 fatcat:mdg6hwug45g2vng657bxianvnq

Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks

Guishan Zhang, Tian Zeng, Zhiming Dai, Xianhua Dai
2021 Computational and Structural Biotechnology Journal  
Thus, optimized design of sgRNAs by maximizing their on-target activity and minimizing their potential off-target mutations are crucial concerns for this system.  ...  A key prerequisite for the success of CRISPR/Cas9 is its capacity to distinguish between single guide RNAs (sgRNAs) on target and homologous off-target sites.  ...  Author's contributions All authors contributed to the project design. GSZ and TZ wrote the analysis source code, analyzed the data. GSZ drafted the full manuscript.  ... 
doi:10.1016/j.csbj.2021.03.001 pmid:33841753 pmcid:PMC8010402 fatcat:tfryfvi6gbczrfio7h5dqneoq4
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