Department of Bioengineering, Stanford University, 450 Serra Mall, Stanford, 94305, USA.
Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305, USA.
Genome Biol. 2020 Mar 9;21(1):62. doi: 10.1186/s13059-020-01972-x.
Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.
全基因组 CRISPR-Cas 介导的敲除、激活和抑制筛选是功能基因组研究的有力工具。尽管它们越来越重要，但目前关于如何设计和分析 CRISPR 池筛选的指导很少。在这里，我们提供了对 pooled CRISPR 筛选的计算分析中常用算法的综述。我们开发了一个全面的模拟框架，使用合成和真实数据集来基准测试和比较这些算法的性能。我们的研究结果为 CRISPR 筛选提供了参数选择的信息，并为研究人员在 pooled CRISPR 筛选的设计和分析方面提供了指导。
