AlleleProfileR: A versatile tool to identify and profile sequence variants in edited genomes

被引：4

作者：

Bruyneel, Arne A. N. ^{[1
,2
]}

Colas, Alexandre R. ^{[3
]}

Karakikes, Ioannis ^{[1
,4
]}

Mercola, Mark ^{[1
,2
]}

机构：

[1] Stanford Sch Med, Stanford Cardiovasc Inst, Stanford, CA 94305 USA

[2] Stanford Sch Med, Dept Med, Div Cardiovasc Med, Stanford, CA 94305 USA

[3] Sanford Burnham Prebys Med Discovery Inst, La Jolla, CA USA

[4] Stanford Sch Med, Dept Cardiothorac Surg, Stanford, CA 94305 USA

来源：

PLOS ONE | 2019年 / 14卷 / 12期

基金：

美国国家卫生研究院;

关键词：

DNA; KNOCKOUT; BASE; ANALYZER; GENES; RNA;

D O I：

10.1371/journal.pone.0226694

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Gene editing strategies, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9), are revolutionizing biology. However, quantitative and sensitive detection of targeted mutations are required to evaluate and quantify the genome editing outcomes. Here we present AlleleProfileR, a new analysis tool, written in a combination of R and C++, with the ability to batch process the sequence analysis of large and complex genome editing experiments, including the recently developed base editing technologies.

引用

页数：11

共 31 条

[21] FLASH: fast length adjustment of short reads to improve genome assemblies [J].

Magoc, Tanja ;

Salzberg, Steven L. .

BIOINFORMATICS, 2011, 27 (21) :2957-2963

[22] Cas-analyzer: an online tool for assessing genome editing results using NGS data [J].

Park, Jeongbin ;

Lim, Kayeong ;

Kim, Jin-Soo ;

Bae, Sangsu .

BIOINFORMATICS, 2017, 33 (02) :286-288

[23] Analyzing CRISPR genome-editing experiments with CRISPResso [J].

Pinello, Luca ;

Canver, Matthew C. ;

Hoban, Megan D. ;

Orkin, Stuart H. ;

Kohn, Donald B. ;

Bauer, Daniel E. ;

Yuan, Guo-Cheng .

NATURE BIOTECHNOLOGY, 2016, 34 (07) :695-697

[24] The combinational use of CRISPR/Cas9-based gene editing and targeted toxin technology enables efficient biallelic knockout of the-1,3-galactosyltransferase gene in porcine embryonic fibroblasts [J].

Sato, Masahiro ;

Miyoshi, Kazuchika ;

Nagao, Yozo ;

Nishi, Yohei ;

Ohtsuka, Masato ;

Nakamura, Shingo ;

Sakurai, Takayuki ;

Watanabe, Satoshi .

XENOTRANSPLANTATION, 2014, 21 (03) :291-300

[25] Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells [J].

Shalem, Ophir ;

Sanjana, Neville E. ;

Hartenian, Ella ;

Shi, Xi ;

Scott, David A. ;

Mikkelsen, Tarjei S. ;

Heckl, Dirk ;

Ebert, Benjamin L. ;

Root, David E. ;

Doench, John G. ;

Zhang, Feng .

SCIENCE, 2014, 343 (6166) :84-87

[26]

Vu T, 2013, J THROMB HAEMOST, V11, P20

[27] ggseqlogo: a versatile R package for drawing sequence logos [J].

Wagih, Omar .

BIOINFORMATICS, 2017, 33 (22) :3645-3647

[28] One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering [J].

Wang, Haoyi ;

Yang, Hui ;

Shivalila, Chikdu S. ;

Dawlaty, Meelad M. ;

Cheng, Albert W. ;

Zhang, Feng ;

Jaenisch, Rudolf .

CELL, 2013, 153 (04) :910-918

[29] CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline [J].

Wang, Xuning ;

Tilford, Charles ;

Neuhaus, Isaac ;

Mintier, Gabe ;

Guo, Qi ;

Feder, John N. ;

Kirov, Stefan .

BIOINFORMATICS, 2017, 33 (23) :3811-3812

[30] AGEseq: Analysis of Genome Editing by Sequencing [J].

Xue, Liang-Jiao ;

Tsai, Chung-Jui .

MOLECULAR PLANT, 2015, 8 (09) :1428-1430

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