DeepCRISPR: optimized CRISPR guide RNA design by deep learning

被引：265

作者：

Chuai, Guohui ^{[1
,2
]}

Ma, Hanhui ^{[5
]}

Yan, Jifang ^{[1
,2
]}

Chen, Ming ^{[4
]}

Hong, Nanfang ^{[1
,2
]}

Xue, Dongyu ^{[1
,2
]}

Zhou, Chi ^{[1
,2
]}

Zhu, Chenyu ^{[1
,2
]}

Chen, Ke ^{[1
,2
]}

Duan, Bin ^{[1
,2
]}

Gu, Feng ^{[6
,7
,8
]}

Qu, Sheng ^{[1
,2
]}

Huang, Deshuang ^{[3
]}

Wei, Jia ^{[4
]}

Liu, Qi ^{[1
,2
]}

机构：

[1] Tongji Univ, Dept Endocrinol & Metab, Shanghai Peoples Hosp 10, Shanghai 20009, Peoples R China

[2] Tongji Univ, Sch Life Sci & Technol, Bioinformat Dept, Shanghai 20009, Peoples R China

[3] Tongji Univ, Sch Elect & Informat Engn, Machine Learning & Syst Biol Lab, Shanghai 201804, Peoples R China

[4] AstraZeneca, Innovat Ctr China, R&D Informat, 199 Liangjing Rd, Shanghai 201203, Peoples R China

[5] ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China

[6] Wenzhou Med Univ, State Key Lab Cultivat Base, Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China

[7] Wenzhou Med Univ, Key Lab Vis Sci, Minist Hlth, Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China

[8] Wenzhou Med Univ, Zhejiang Prov Key Lab Ophthalmol & Optometry, Sch Ophthalmol & Optometry, Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China

来源：

GENOME BIOLOGY | 2018年 / 19卷

基金：

中国国家自然科学基金;

关键词：

CRISPR system; Gene knockout; Deep learning; On-targets; Off-targets; OFF-TARGET CLEAVAGE; GENOME; SEQ; DNA; SPECIFICITIES; PREDICTION; NUCLEASES; SELECTION; SGRNAS;

D O I：

10.1186/s13059-018-1459-4

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized design of sgRNAs with high sensitivity and specificity. Here we present DeepCRISPR, a comprehensive computational platform to unify sgRNA on-target and off-target site prediction into one framework with deep learning, surpassing available state-of-the-art in silico tools. In addition, DeepCRISPR fully automates the identification of sequence and epigenetic features that may affect sgRNA knockout efficacy in a data-driven manner. DeepCRISPR is available at http://www.deeperispr.net/.

引用

页数：18

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