Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing

Disrupting the adult-globin promoter alleviates promoter competition and reactivates foetal-globin gene expression

(2022) Sarah Topfer et al.   BLOOD

Promoter competition in globin gene control

(2022) Ross C. Hardison   BLOOD

Highly efficient PD-1-targeted CRISPR-Cas9 for tumor-infiltrating lymphocyte-based adoptive T cell therapy

(2022) Christopher Aled Chamberlain et al.   Molecular Therapy-Oncolytics

Cas9-induced large deletions and small indels are controlled in a convergent fashion

(2022) Michael Kosicki et al.   Nature Communications

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

(2021) Søren M. Karst et al.   NATURE METHODS

Simple and reliable detection of CRISPR-induced on-target effects by qgPCR and SNP genotyping

(2021) Isabel Weisheit et al.   Nature Protocols

CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis

(2021) Julian D. Gillmore et al.   NEW ENGLAND JOURNAL OF MEDICINE

Development of β-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease

(2021) Annalisa Lattanzi et al.   Science Translational Medicine

3′HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression

(2021) Pamela Himadewi et al.   eLife

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

(2020) Pieter Spealman et al.   NUCLEIC ACIDS RESEARCH

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

Rational selection of CRISPR/Cas9 guide RNAs for homology directed genome editing

(2020) Kristina J. Tatiossian et al.   MOLECULAR THERAPY

A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break repair choice

(2020) Paris Roidos et al.   Nature Communications

Large-Fragment Deletions Induced by Cas9 Cleavage while Not in the BEs System

(2020) Yuning Song et al.   Molecular Therapy-Nucleic Acids

Tools for experimental and computational analyses of off-target editing by programmable nucleases

(2020) X. Robert Bao et al.   Nature Protocols

Dynamics and competition of CRISPR–Cas9 ribonucleoproteins and AAV donor-mediated NHEJ, MMEJ and HDR editing

(2020) Ya-Wen Fu et al.   NUCLEIC ACIDS RESEARCH

Highly efficient therapeutic gene editing of human hematopoietic stem cells

(2019) Yuxuan Wu et al.   NATURE MEDICINE

Microhomologies are prevalent at Cas9-induced larger deletions

(2019) Dominic D G Owens et al.   NUCLEIC ACIDS RESEARCH

Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease

(2019) So Hyun Park et al.   NUCLEIC ACIDS RESEARCH

Therapeutically relevant engraftment of a CRISPR-Cas9–edited HSC-enriched population with HbF reactivation in nonhuman primates

(2019) Olivier Humbert et al.   Science Translational Medicine

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Molecular basis of β thalassemia and potential therapeutic targets

(2018) Swee Lay Thein   BLOOD CELLS MOLECULES AND DISEASES

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

Large deletions induced by Cas9 cleavage

(2018) Fatwa Adikusuma et al.   NATURE

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

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

(2018) Ryan R. Wick et al.   PLoS Computational Biology

CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome

(2017) Ha Youn Shin et al.   Nature Communications

Efficient Recreation of t(11;22) EWSR1-FLI1 + in Human Stem Cells Using CRISPR/Cas9

(2017) Raul Torres-Ruiz et al.   Stem Cell Reports

Long-Term Engraftment and Fetal Globin Induction upon BCL11A Gene Editing in Bone-Marrow-Derived CD34 + Hematopoietic Stem and Progenitor Cells

(2017) Kai-Hsin Chang et al.   Molecular Therapy-Methods & Clinical Development

Nanopore sequencing detects structural variants in cancer

(2016) Alexis L. Norris et al.   CANCER BIOLOGY & THERAPY

CRISPR/Cas9 β-globin gene targeting in human haematopoietic stem cells

(2016) Daniel P. Dever et al.   NATURE

Analyzing CRISPR genome-editing experiments with CRISPResso

(2016) Luca Pinello et al.   NATURE BIOTECHNOLOGY

Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells

(2016) M. A. DeWitt et al.   Science Translational Medicine

Correction of the sickle cell disease mutation in human hematopoietic stem/progenitor cells

(2015) M. D. Hoban et al.   BLOOD

Therapeutic genome editing: prospects and challenges

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

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Quantifying Genome-Editing Outcomes at Endogenous Loci with SMRT Sequencing

(2014) Ayal Hendel et al.   Cell Reports

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

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

Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells

(2013) Ryo Kurita et al.   PLoS One

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS