Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency

(2020) Kasidet Hiranniramol et al.   BIOINFORMATICS

Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses

(2020) Jonathan M. Levy et al.   Nature Biomedical Engineering

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

(2020) Michelle F. Richter et al.   NATURE BIOTECHNOLOGY

CRISPR off-target detection with DISCOVER-seq

(2020) Beeke Wienert et al.   Nature Protocols

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Suppression of unwanted CRISPR-Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs

(2020) John C. Rose et al.   Nature Communications

Polyethylenimine based magnetic nanoparticles mediated non-viral CRISPR/Cas9 system for genome editing

(2020) S. S. Rohiwal et al.   Scientific Reports

Successful delivery of large-size CRISPR/Cas9 vectors in hard-to-transfect human cells using small plasmids

(2020) Jonas Nørskov Søndergaard et al.   Communications Biology

Crisflash: Open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation

(2019) Adrien LS Jacquin et al.   BIOINFORMATICS

CRISPR-based RNA editing: diagnostic applications and therapeutic options

(2019) Diana Gulei et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Clinical applications of CRISPR-based genome editing and diagnostics

(2019) Dana V. Foss et al.   TRANSFUSION

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

(2019) Erwei Zuo et al.   SCIENCE

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

(2019) Shuai Jin et al.   SCIENCE

Efficient Human Genome Editing Using SaCas9 Ribonucleoprotein Complexes

(2019) Yufei Wang et al.   Biotechnology Journal

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

Increasing the specificity of CRISPR systems with engineered RNA secondary structures

(2019) D. Dewran Kocak et al.   NATURE BIOTECHNOLOGY

Evaluation and Reduction of CRISPR Off-Target Cleavage Events

(2019) Christopher A. Vakulskas et al.   Nucleic Acid Therapeutics

Analysis and minimization of cellular RNA editing by DNA adenine base editors

(2019) Holly A. Rees et al.   Science Advances

Strategies to Increase On-Target and Reduce Off-Target Effects of the CRISPR/Cas9 System in Plants

(2019) Zahra Hajiahmadi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

(2019) Changyang Zhou et al.   NATURE

Advances in Detecting and Reducing Off-target Effects Generated by CRISPR-mediated Genome Editing

(2019) Jin-Jing Li et al.   Journal of Genetics and Genomics

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

High levels of AAV vector integration into CRISPR-induced DNA breaks

(2019) Killian S. Hanlon et al.   Nature Communications

FlashFry: a fast and flexible tool for large-scale CRISPR target design

(2018) Aaron McKenna et al.   BMC BIOLOGY

Delivering CRISPR: a review of the challenges and approaches

(2018) Christopher A. Lino et al.   DRUG DELIVERY

Base editing with a Cpf1–cytidine deaminase fusion

(2018) Xiaosa Li et al.   NATURE BIOTECHNOLOGY

Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction

(2018) Luke W Koblan et al.   NATURE BIOTECHNOLOGY

A highly specific SpCas9 variant is identified by in vivo screening in yeast

(2018) Antonio Casini et al.   NATURE BIOTECHNOLOGY

Partial DNA-guided Cas9 enables genome editing with reduced off-target activity

(2018) Hao Yin et al.   Nature Chemical Biology

CRISPR off-target analysis in genetically engineered rats and mice

(2018) Keith R. Anderson et al.   NATURE METHODS

Engineering altered protein–DNA recognition specificity

(2018) Adam J Bogdanove et al.   NUCLEIC ACIDS RESEARCH

Identifying and avoiding off-target effects of RNase H-dependent antisense oligonucleotides in mice

(2018) Peter H Hagedorn et al.   NUCLEIC ACIDS RESEARCH

Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity

(2018) Christopher R. Cromwell et al.   Nature Communications

The Current State and Future of CRISPR-Cas9 gRNA Design Tools

(2018) Laurence O. W. Wilson et al.   Frontiers in Pharmacology

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs

(2018) Jennifer Listgarten et al.   Nature Biomedical Engineering

In vivo CRISPR editing with no detectable genome-wide off-target mutations

(2018) Pinar Akcakaya et al.   NATURE

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion

(2018) Xiao Wang et al.   NATURE BIOTECHNOLOGY

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

(2018) Jason M Gehrke et al.   NATURE BIOTECHNOLOGY

A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells

(2018) Christopher A. Vakulskas et al.   NATURE MEDICINE

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

Directed evolution of CRISPR-Cas9 to increase its specificity

(2018) Jungjoon K. Lee et al.   Nature Communications

CRISPR/Cas9-Mediated Deletion of Large Genomic Fragments in Soybean

(2018) Yupeng Cai et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Gesicle-Mediated Delivery of CRISPR/Cas9 Ribonucleoprotein Complex for Inactivating the HIV Provirus

(2018) Lee A. Campbell et al.   MOLECULAR THERAPY

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha

(2018) Shigeo S. Sugano et al.   PLoS One

The Development of an AAV-Based CRISPR SaCas9 Genome Editing System That Can Be Delivered to Neurons in vivo and Regulated via Doxycycline and Cre-Recombinase

(2018) Namrata Kumar et al.   Frontiers in Molecular Neuroscience

Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65 -mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial

(2017) Stephen Russell et al.   LANCET

Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells

(2017) Steven Havlicek et al.   MOLECULAR THERAPY

Enhanced proofreading governs CRISPR–Cas9 targeting accuracy

(2017) Janice S. Chen et al.   NATURE

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

GuideScan software for improved single and paired CRISPR guide RNA design

(2017) Alexendar R Perez et al.   NATURE BIOTECHNOLOGY

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Mapping the genomic landscape of CRISPR–Cas9 cleavage

(2017) Peter Cameron et al.   NATURE METHODS

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets

(2017) Shengdar Q Tsai et al.   NATURE METHODS

Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs

(2017) Daniel E Ryan et al.   NUCLEIC ACIDS RESEARCH

In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni

(2017) Eunji Kim et al.   Nature Communications

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

(2017) Holly A. Rees et al.   Nature Communications

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action

(2017) Shiran Abadi et al.   PLoS Computational Biology

A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9

(2017) Yavuz S. Dagdas et al.   Science Advances

Disabling Cas9 by an anti-CRISPR DNA mimic

(2017) Jiyung Shin et al.   Science Advances

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

Structure and Engineering of Francisella novicida Cas9

(2016) Hisato Hirano et al.   CELL

The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells

(2016) Ciaran M Lee et al.   MOLECULAR THERAPY

A Self-restricted CRISPR System to Reduce Off-target Effects

(2016) Yanhao Chen et al.   MOLECULAR THERAPY

Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome

(2016) Maximilian Müller et al.   MOLECULAR THERAPY

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins

(2016) Junho K Hur et al.   NATURE BIOTECHNOLOGY

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing

(2016) Jiazhi Hu et al.   Nature Protocols

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins

(2016) Saminathan Subburaj et al.   PLANT CELL REPORTS

Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles

(2016) Ming Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes

(2016) C. D. Richardson et al.   Nature Communications

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9

(2016) Digvijay Singh et al.   Nature Communications

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

(2016) James I. McDonald et al.   Biology Open

CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.)

(2016) Chong Ren et al.   Scientific Reports

Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing

(2015) Nicolas Wyvekens et al.   HUMAN GENE THERAPY

Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection

(2015) Xiquan Liang et al.   JOURNAL OF BIOTECHNOLOGY

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition

(2015) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors

(2015) Xiaoling Wang et al.   NATURE BIOTECHNOLOGY

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells

(2015) Daesik Kim et al.   NATURE METHODS

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation

(2015) Levi G. Lowder et al.   PLANT PHYSIOLOGY

Targeted gene editing by transfection ofin vitroreconstitutedStreptococcus thermophilusCas9 nuclease complex

(2015) Monika Glemzaite et al.   RNA Biology

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells

(2015) Hsin-Kai Liao et al.   Nature Communications

CRISPR/gRNA-directed synergistic activation mediator (SAM) induces specific, persistent and robust reactivation of the HIV-1 latent reservoirs

(2015) Yonggang Zhang et al.   Scientific Reports

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

(2015) Manuel Stemmer et al.   PLoS One

CasOT: a genome-wide Cas9/gRNA off-target searching tool

(2014) A. Xiao et al.   BIOINFORMATICS

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Efficient genome engineering in eukaryotes using Cas9 from Streptococcus thermophilus

(2014) Kun Xu et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo

(2014) John A Zuris et al.   NATURE BIOTECHNOLOGY

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew

(2014) Yanpeng Wang et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

(2014) Cem Kuscu et al.   NATURE BIOTECHNOLOGY

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification

(2014) John P Guilinger et al.   NATURE BIOTECHNOLOGY

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity

(2014) John P Guilinger et al.   NATURE METHODS

Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV

(2014) Pablo Tebas et al.   NEW ENGLAND JOURNAL OF MEDICINE

CRISPR-based self-cleaving mechanism for controllable gene delivery in human cells

(2014) Richard Moore et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences

(2014) Y. Lin et al.   NUCLEIC ACIDS RESEARCH

Multigene Knockout Utilizing Off-Target Mutations of the CRISPR/Cas9 System in Rice

(2014) Masaki Endo et al.   PLANT AND CELL PHYSIOLOGY

Enhanced Specificity and Efficiency of the CRISPR/Cas9 System with Optimized sgRNA Parameters in Drosophila

(2014) Xingjie Ren et al.   Cell Reports

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

(2013) Vikram Pattanayak et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis

(2013) Z. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

An unbiased genome-wide analysis of zinc-finger nuclease specificity

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

Frequent Endonuclease Cleavage at Off-target Locations In Vivo

(2010) Lisa M Petek et al.   MOLECULAR THERAPY

Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

(2009) Aimee L. Jackson et al.   NATURE REVIEWS DRUG DISCOVERY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY