Minimizing off-Target Mutagenesis Risks Caused by Programmable Nucleases

From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing

(2015) Akitsu Hotta et al.   Annual Review of Genetics

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1.

(2015) Honglei Liu et al.   BIOINFORMATICS

Functional Correction of Large Factor VIII Gene Chromosomal Inversions in Hemophilia A Patient-Derived iPSCs Using CRISPR-Cas9

(2015) Chul-Yong Park et al.   Cell Stem Cell

Measuring and Reducing Off-Target Activities of Programmable Nucleases Including CRISPR-Cas9

(2015) Taeyoung Koo et al.   MOLECULES AND CELLS

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells

(2015) Ayal Hendel et al.   NATURE BIOTECHNOLOGY

Flexible guide-RNA design for CRISPR applications using Protospacer Workbench

(2015) Cameron Ross MacPherson 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

Small molecule–triggered Cas9 protein with improved genome-editing specificity

(2015) Kevin M Davis et al.   Nature Chemical Biology

Off-target mutations are rare in Cas9-modified mice

(2015) Vivek Iyer et al.   NATURE METHODS

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

(2015) Raj Chari 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

A Cas9-guide RNA complex preorganized for target DNA recognition

(2015) F. Jiang et al.   SCIENCE

Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy

(2015) Ioannis Karakikes et al.   Nature Communications

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/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus

(2015) Vyas Ramanan et al.   Scientific Reports

Precise Correction of the Dystrophin Gene in Duchenne Muscular Dystrophy Patient Induced Pluripotent Stem Cells by TALEN and CRISPR-Cas9

(2015) Hongmei Lisa Li et al.   Stem Cell Reports

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

GT-Scan: identifying unique genomic targets

(2014) A. O'Brien et al.   BIOINFORMATICS

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

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

Targeted Gene Correction Minimally Impacts Whole-Genome Mutational Load in Human-Disease-Specific Induced Pluripotent Stem Cell Clones

(2014) Keiichiro Suzuki et al.   Cell Stem Cell

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

(2014) Adrian Veres et al.   Cell Stem Cell

Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs

(2014) Cory Smith et al.   Cell Stem Cell

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Off-target assessment of CRISPR-Cas9 guiding RNAs in human iPS and mouse ES cells

(2014) E-Pien Tan et al.   GENESIS

Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 andpiggyBac

(2014) Fei Xie et al.   GENOME RESEARCH

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells

(2014) Matthew C. Canver et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants

(2014) Yang Lei et al.   Molecular Plant

Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

(2014) Carolin Anders et al.   NATURE

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

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

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

(2014) Shengdar Q Tsai 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 editing with Cas9 in adult mice corrects a disease mutation and phenotype

(2014) Hao Yin 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

Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects

(2014) Bin Shen et al.   NATURE METHODS

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

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

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites

(2014) Shengsong Xie et al.   PLoS One

Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

(2014) James A. Gagnon et al.   PLoS One

Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection

(2014) Lin Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA

(2014) C. Long et al.   SCIENCE

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

Effective gene targeting in rabbits using RNA-guided Cas9 nucleases

(2014) Dongshan Yang et al.   Journal of Molecular Cell Biology

Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells

(2014) Yilan Zhang et al.   Scientific Reports

Targeting Hepatitis B Virus With CRISPR/Cas9

(2014) Christoph Seeger et al.   Molecular Therapy-Nucleic Acids

COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

(2014) Thomas J Cradick et al.   Molecular Therapy-Nucleic Acids

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

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

(2013) F. Ann Ran et al.   CELL

Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos

(2013) Nannan Chang et al.   CELL RESEARCH

Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients

(2013) Gerald Schwank et al.   Cell Stem Cell

Correction of a Genetic Disease in Mouse via Use of CRISPR-Cas9

(2013) Yuxuan Wu et al.   Cell Stem Cell

Genetic correction using engineered nucleases for gene therapy applications

(2013) Hongmei Lisa Li et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Heritable Custom Genomic Modifications in Caenorhabditis elegans via a CRISPR–Cas9 System

(2013) Yonatan B. Tzur et al.   GENETICS

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

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

Reading Frame Correction by Targeted Genome Editing Restores Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients

(2013) David G Ousterout et al.   MOLECULAR THERAPY

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

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

Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems

(2013) Wei Li et al.   NATURE BIOTECHNOLOGY

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

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Heritable gene targeting in the mouse and rat using a CRISPR-Cas system

(2013) Dali Li et al.   NATURE BIOTECHNOLOGY

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

(2013) Nicola Crosetto et al.   NATURE METHODS

Heritable genome editing in C. elegans via a CRISPR-Cas9 system

(2013) Ari E Friedland et al.   NATURE METHODS

CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity

(2013) Thomas J. Cradick et al.   NUCLEIC ACIDS RESEARCH

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus

(2013) Hirotaka Ebina et al.   Scientific Reports

A Guide RNA Sequence Design Platform for the CRISPR/Cas9 System for Model Organism Genomes

(2013) Ming Ma et al.   Biomed Research International

Zscan4 promotes genomic stability during reprogramming and dramatically improves the quality of iPS cells as demonstrated by tetraploid complementation

(2012) Jing Jiang et al.   CELL RESEARCH

Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme

(2012) J. Wang et al.   GENOME RESEARCH

Precision genome engineering with programmable DNA-nicking enzymes

(2012) E. Kim et al.   GENOME RESEARCH

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

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

(2012) M. Jinek et al.   SCIENCE

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells

(2011) Kosuke Yusa et al.   NATURE

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

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes

(2011) Ting Li et al.   NUCLEIC ACIDS RESEARCH

A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity

(2011) Claudio Mussolino et al.   NUCLEIC ACIDS RESEARCH

ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool

(2010) J. D. Sander et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases

(2007) Tatjana I Cornu et al.   MOLECULAR THERAPY