Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants

Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”

(2018) Sang-Tae Kim et al.   NATURE METHODS

Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”

(2018) Caleb A Lareau et al.   NATURE METHODS

Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”

(2018) Christopher J Wilson et al.   NATURE METHODS

Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation (SRA) process

(2018) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Activities and specificities of CRISPR-Cas9 and Cas12a nucleases for targeted mutagenesis in maize

(2018) Keunsub Lee et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Implications of human genetic variation in CRISPR-based therapeutic genome editing

(2017) David A Scott et al.   NATURE MEDICINE

Unexpected mutations after CRISPR–Cas9 editing in vivo

(2017) Kellie A Schaefer et al.   NATURE METHODS

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

High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum ) using CRISPR/Cas9 system

(2017) Pengcheng Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci

(2017) Samuel Lessard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contributions of Zea mays subspecies mexicana haplotypes to modern maize

(2017) Ning Yang et al.   Nature Communications

Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion

(2017) Vladimir Nekrasov et al.   Scientific Reports

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

(2016) Josh Tycko et al.   MOLECULAR CELL

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

Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insectBemisia tabaci(whitefly)

(2016) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

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

(2015) Daesik Kim et al.   NATURE METHODS

Cas9-Guide RNA Directed Genome Editing in Soybean

(2015) Zhongsen Li et al.   PLANT PHYSIOLOGY

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

(2014) Cem Kuscu 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

The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation

(2014) Hui Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis

(2014) Z. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

Targeted mutagenesis in rice using CRISPR-Cas system

(2013) Jin Miao et al.   CELL RESEARCH

Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System

(2013) Zhen Liang et al.   Journal of Genetics and Genomics

Application of the CRISPR–Cas System for Efficient Genome Engineering in Plants

(2013) Yanfei Mao et al.   Molecular Plant

RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System

(2013) Kabin Xie et al.   Molecular Plant

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

BatMis: a fast algorithm for k-mismatch mapping

(2012) Chandana Tennakoon et al.   BIOINFORMATICS

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

(2012) M. Jinek et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes

(2011) Caifu Jiang et al.   CURRENT BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Detection of somaclonal variation of cotton (Gossypium hirsutum) using cytogenetics, flow cytometry and molecular markers

(2008) Shuangxia Jin et al.   PLANT CELL REPORTS