CRISPulator: a discrete simulation tool for pooled genetic screens

BMC Bioinformatics

Software

Martin Kampmann¹  Tamas Nagy² 

[1] Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases and California Institute for Quantitative Biomedical Research, University of California, 94158, San Francisco, CA, USA;Chan Zuckerberg Biohub, 94158, San Francisco, CA, USA;Graduate program in Bioinformatics, University of California, 94158, San Francisco, CA, USA;

关键词: CRISPR;    CRISPRi;    Functional genomics;    Genome-wide screens;    Simulation;    Monte Carlo;   

DOI  :  10.1186/s12859-017-1759-9

 received in 2017-03-17, accepted in 2017-07-13,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe rapid adoption of CRISPR technology has enabled biomedical researchers to conduct CRISPR-based genetic screens in a pooled format. The quality of results from such screens is heavily dependent on the selection of optimal screen design parameters, which also affects cost and scalability. However, the cost and effort of implementing pooled screens prohibits experimental testing of a large number of parameters.ResultsWe present CRISPulator, a Monte Carlo method-based computational tool that simulates the impact of screen parameters on the robustness of screen results, thereby enabling users to build intuition and insights that will inform their experimental strategy.CRISPulator enables the simulation of screens relying on either CRISPR interference (CRISPRi) or CRISPR nuclease (CRISPRn). Pooled screens based on cell growth/survival, as well as fluorescence-activated cell sorting according to fluorescent reporter phenotypes are supported. CRISPulator is freely available online (http://crispulator.ucsf.edu).ConclusionsCRISPulator facilitates the design of pooled genetic screens by enabling the exploration of a large space of experimental parameters in silico, rather than through costly experimental trial and error. We illustrate its power by deriving non-obvious rules for optimal screen design.

【 授权许可】

CC BY   
© The Author(s). 2017