Cas-analyzer: an online tool for assessing genome editing results using NGS data

被引：294

作者：

Park, Jeongbin ^{[1
,5
]}

Lim, Kayeong ^{[2
,3
]}

Kim, Jin-Soo ^{[2
,3
]}

Bae, Sangsu ^{[1
,4
]}

机构：

[1] Hanyang Univ, Dept Chem, Seoul, South Korea

[2] Inst for Basic Sci Korea, Ctr Genome Engn, Seoul, South Korea

[3] Seoul Natl Univ, Dept Chem, Seoul, South Korea

[4] Hanyang Univ, Res Inst Convergence Basic Sci, Seoul, South Korea

[5] German Canc Res Ctr, Div Theoret Bioinformat, Heidelberg, Germany

来源：

BIOINFORMATICS | 2017年 / 33卷 / 02期

关键词：

RNA-GUIDED ENDONUCLEASE; ZINC-FINGER NUCLEASES; HUMAN-CELLS; CPF1; RIBONUCLEOPROTEINS; SPECIFICITY; KNOCKOUT; SYSTEM; MICE;

D O I：

10.1093/bioinformatics/btw561

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

引用

页码：286 / 288

页数：3

共 25 条

[1] DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins [J].

Baek, Kwangryul ;

Kim, Duk Hyoung ;

Jeong, Jooyeon ;

Sim, Sang Jun ;

Melis, Anastasios ;

Kim, Jin-Soo ;

Jin, EonSeon ;

Bae, Sangsu .

SCIENTIFIC REPORTS, 2016, 6

[2] Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases [J].

Cho, Seung Woo ;

Kim, Sojung ;

Kim, Yongsub ;

Kweon, Jiyeon ;

Kim, Heon Seok ;

Bae, Sangsu ;

Kim, Jin-Soo .

GENOME RESEARCH, 2014, 24 (01) :132-141

[3] Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease [J].

Cho, Seung Woo ;

Kim, Sojung ;

Kim, Jong Min ;

Kim, Jin-Soo .

NATURE BIOTECHNOLOGY, 2013, 31 (03) :230-232

[4] Multiplex Genome Engineering Using CRISPR/Cas Systems [J].

Cong, Le ;

Ran, F. Ann ;

Cox, David ;

Lin, Shuailiang ;

Barretto, Robert ;

Habib, Naomi ;

Hsu, Patrick D. ;

Wu, Xuebing ;

Jiang, Wenyan ;

Marraffini, Luciano A. ;

Zhang, Feng .

SCIENCE, 2013, 339 (6121) :819-823

[5] Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA) [J].

Gueell, Marc ;

Yang, Luhan ;

Church, George M. .

BIOINFORMATICS, 2014, 30 (20) :2968-2970

[6] Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis [J].

Hou, Zhonggang ;

Zhang, Yan ;

Propson, Nicholas E. ;

Howden, Sara E. ;

Chu, Li-Fang ;

Sontheimer, Erik J. ;

Thomson, James A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (39) :15644-15649

[7] Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins [J].

Hur, Junho K. ;

Kim, Kyoungmi ;

Been, Kyung Wook ;

Baek, Gayoung ;

Ye, Sunghyeok ;

Hur, Junseok W. ;

Ryu, Seuk-Min ;

Lee, Youn Su ;

Kim, Jin-Soo .

NATURE BIOTECHNOLOGY, 2016, 34 (08) :807-808

[8] RNA-programmed genome editing in human cells [J].

Jinek, Martin ;

East, Alexandra ;

Cheng, Aaron ;

Lin, Steven ;

Ma, Enbo ;

Doudna, Jennifer .

ELIFE, 2013, 2

[9]

Kim D, 2016, NAT BIOTECHNOL, V34, P863, DOI 10.1038/nbt.3609

[10] Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly [J].

Kim, Hye Joo ;

Lee, Hyung Joo ;

Kim, Hyojin ;

Cho, Seung Woo ;

Kim, Jin-Soo .

GENOME RESEARCH, 2009, 19 (07) :1279-1288

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