Genome engineering tools for building cellular models of disease

Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing

(2016) Ciaran M Lee et al.   MOLECULAR THERAPY

Deriving human ENS lineages for cell therapy and drug discovery in Hirschsprung disease

(2016) Faranak Fattahi et al.   NATURE

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

DNA-guided genome editing using the Natronobacterium gregoryi Argonaute

(2016) Feng Gao et al.   NATURE BIOTECHNOLOGY

Human neural crest cells contribute to coat pigmentation in interspecies chimeras after in utero injection into mouse embryos

(2016) Malkiel A. Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Disease Modeling Reveals Integrated Transcriptional and Epigenetic Mechanisms of NOTCH1 Haploinsufficiency

(2015) Christina V. Theodoris et al.   CELL

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Knockout ofAdamts7, a Novel Coronary Artery Disease Locus in Humans, Reduces Atherosclerosis in MiceCLINICAL PERSPECTIVE

(2015) Robert C. Bauer et al.   CIRCULATION

Functional Analysis and Transcriptomic Profiling of iPSC-Derived Macrophages and Their Application in Modeling Mendelian Disease

(2015) H. Zhang et al.   CIRCULATION RESEARCH

The Precision Medicine Initiative

(2015) Euan A. Ashley   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Tribbles-1 regulates hepatic lipogenesis through posttranscriptional regulation of C/EBPα

(2015) Robert C. Bauer et al.   JOURNAL OF CLINICAL INVESTIGATION

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

A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease

(2015) Majid Nikpay et al.   NATURE GENETICS

Therapeutic genome editing: prospects and challenges

(2015) David Benjamin Turitz Cox et al.   NATURE MEDICINE

Improved specificity of TALE-based genome editing using an expanded RVD repertoire

(2015) Jeffrey C Miller et al.   NATURE METHODS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Rationally engineered Cas9 nucleases with improved specificity

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

Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy

(2015) C. Long et al.   SCIENCE

In vivo gene editing in dystrophic mouse muscle and muscle stem cells

(2015) M. Tabebordbar et al.   SCIENCE

In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy

(2015) C. E. Nelson et al.   SCIENCE

Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs

(2015) Amy L. Firth et al.   Cell Reports

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

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

(2014) E-Pien Tan et al.   GENESIS

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

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

(2014) John P Guilinger et al.   NATURE BIOTECHNOLOGY

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

(2014) Anubha Mahajan et al.   NATURE GENETICS

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

(2014) John P Guilinger et al.   NATURE METHODS

Long-Term Safety and Efficacy of Factor IX Gene Therapy in Hemophilia B

(2014) Amit C. Nathwani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

(2014) Luhan Yang et al.   Nature Communications

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

(2014) Yilan Zhang et al.   Scientific Reports

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

(2013) F. Ann Ran et al.   CELL

Genetic Correction of a LRRK2 Mutation in Human iPSCs Links Parkinsonian Neurodegeneration to ERK-Dependent Changes in Gene Expression

(2013) Peter Reinhardt et al.   Cell Stem Cell

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

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

A library of TAL effector nucleases spanning the human genome

(2013) Yongsub Kim et al.   NATURE BIOTECHNOLOGY

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

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

Common variants associated with plasma triglycerides and risk for coronary artery disease

(2013) Ron Do et al.   NATURE GENETICS

Validating therapeutic targets through human genetics

(2013) Robert M. Plenge et al.   NATURE REVIEWS DRUG DISCOVERY

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

(2012) Kristopher L. Nazor et al.   Cell Stem Cell

Genetic Correction of Huntington's Disease Phenotypes in Induced Pluripotent Stem Cells

(2012) Mahru C. An et al.   Cell Stem Cell

Highly active zinc-finger nucleases by extended modular assembly

(2012) M. S. Bhakta et al.   GENOME RESEARCH

Progressive degeneration of human neural stem cells caused by pathogenic LRRK2

(2012) Guang-Hui Liu et al.   NATURE

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

Targeted transcriptional activation of silent oct4 pluripotency gene by combining designer TALEs and inhibition of epigenetic modifiers

(2012) Sebastian Bultmann et al.   NUCLEIC ACIDS RESEARCH

Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations

(2011) Frank Soldner et al.   CELL

Targeted Gene Correction of Laminopathy-Associated LMNA Mutations in Patient-Specific iPSCs

(2011) Guang-Hui Liu et al.   Cell Stem Cell

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

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

(2011) Kosuke Yusa et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

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

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection

(2011) Vikram Pattanayak et al.   NATURE METHODS

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

(2011) Koichiro Nishino et al.   PLoS Genetics

Reprogramming of Human Peripheral Blood Cells to Induced Pluripotent Stem Cells

(2010) Judith Staerk et al.   Cell Stem Cell

Generation of Induced Pluripotent Stem Cells from Human Terminally Differentiated Circulating T Cells

(2010) Tomohisa Seki et al.   Cell Stem Cell

Engineering of Human Pluripotent Stem Cells by AAV-mediated Gene Targeting

(2010) Iram F Khan et al.   MOLECULAR THERAPY

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

(2010) Jose M Polo et al.   NATURE BIOTECHNOLOGY

Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)

(2010) Jeffry D Sander et al.   NATURE METHODS

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays

(2009) Morgan L Maeder et al.   Nature Protocols

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

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

Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease

(2009) Sylvestre Grizot et al.   NUCLEIC ACIDS RESEARCH

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Disease-Specific Induced Pluripotent Stem Cells

(2008) In-Hyun Park et al.   CELL

Rapid “Open-Source” Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification

(2008) Morgan L. Maeder et al.   MOLECULAR CELL

Unexpected failure rates for modular assembly of engineered zinc fingers

(2008) Cherie L Ramirez et al.   NATURE METHODS

Highly efficient transient gene expression and gene targeting in primate embryonic stem cells with helper-dependent adenoviral vectors

(2008) K. Suzuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced Pluripotent Stem Cells Generated from Patients with ALS Can Be Differentiated into Motor Neurons

(2008) J. T. Dimos et al.   SCIENCE