CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline

被引：32

作者：

Wang, Xuning ^{[1
]}

Tilford, Charles ^{[1
]}

Neuhaus, Isaac ^{[1
]}

Mintier, Gabe ^{[2
]}

Guo, Qi ^{[3
]}

Feder, John N. ^{[2
]}

Kirov, Stefan ^{[1
]}

机构：

[1] Bristol Myers Squibb Co, Translat Bioinformat & Computat Genom, Pennington, NJ 08534 USA

[2] Bristol Myers Squibb Co, Leads Discovery & Optimizat, Pennington, NJ 08534 USA

[3] Bristol Myers Squibb Co, Genome Biol, Pennington, NJ 08534 USA

来源：

BIOINFORMATICS | 2017年 / 33卷 / 23期

关键词：

GENOME EDITING ASSESSMENT; ANALYZER; REPAIR;

D O I：

10.1093/bioinformatics/btx518

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view.

引用

页码：3811 / 3812

页数：2

共 12 条

[1] A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing [J].

Bell, Charles C. ;

Magor, Graham W. ;

Gillinder, Kevin R. ;

Perkins, Andrew C. .

BMC GENOMICS, 2014, 15

[2] BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment [J].

Boel, Annekatrien ;

Steyaert, Woutert ;

De Rocker, Nina ;

Menten, Bjorn ;

Callewaert, Bert ;

De Paepe, Anne ;

Coucke, Paul ;

Willaert, Andy .

SCIENTIFIC REPORTS, 2016, 6

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

Gueell, Marc ;

Yang, Luhan ;

Church, George M. .

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

[4] Mechanisms of DNA double strand break repair and chromosome aberration formation [J].

Iliakis, G ;

Wang, H ;

Perrault, AR ;

Boecker, W ;

Rosidi, B ;

Windhofer, F ;

Wu, W ;

Guan, J ;

Terzoudi, G ;

Pantelias, G .

CYTOGENETIC AND GENOME RESEARCH, 2004, 104 (1-4) :14-20

[5] The Sequence Alignment/Map format and SAMtools [J].

Li, Heng ;

Handsaker, Bob ;

Wysoker, Alec ;

Fennell, Tim ;

Ruan, Jue ;

Homer, Nils ;

Marth, Gabor ;

Abecasis, Goncalo ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (16) :2078-2079

[6] Fast and accurate short read alignment with Burrows-Wheeler transform [J].

Li, Heng ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (14) :1754-1760

[7] ABRA: improved coding indel detection via assembly-based realignment [J].

Mose, Lisle E. ;

Wilkerson, Matthew D. ;

Hayes, D. Neil ;

Perou, Charles M. ;

Parker, Joel S. .

BIOINFORMATICS, 2014, 30 (19) :2813-2815

[8] 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

[9] Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells [J].

Pierce, AJ ;

Hu, P ;

Han, MG ;

Ellis, N ;

Jasin, M .

GENES & DEVELOPMENT, 2001, 15 (24) :3237-3242

[10] 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

← 1 2 →