European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK.
Wellcome Sanger Institute, Cambridge, UK.
BMC Genomics. 2018 Aug 13;19(1):604. doi: 10.1186/s12864-018-4989-y.
Genome editing by CRISPR-Cas9 technology allows large-scale screening of gene essentiality in cancer. A confounding factor when interpreting CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes within copy number amplified regions of the genome. We have developed the computational tool CRISPRcleanR which is capable of identifying and correcting gene-independent responses to CRISPR-Cas9 targeting. CRISPRcleanR uses an unsupervised approach based on the segmentation of single-guide RNA fold change values across the genome, without making any assumption about the copy number status of the targeted genes.
Applying our method to existing and newly generated genome-wide essentiality profiles from 15 cancer cell lines, we demonstrate that CRISPRcleanR reduces false positives when calling essential genes, correcting biases within and outside of amplified regions, while maintaining true positive rates. Established cancer dependencies and essentiality signals of amplified cancer driver genes are detectable post-correction. CRISPRcleanR reports sgRNA fold changes and normalised read counts, is therefore compatible with downstream analysis tools, and works with multiple sgRNA libraries.
CRISPRcleanR is a versatile open-source tool for the analysis of CRISPR-Cas9 knockout screens to identify essential genes.
CRISPR-Cas9 技术的基因组编辑允许在癌症中大规模筛选基因的必要性。在解释 CRISPR-Cas9 筛选时，一个令人困惑的因素是在基因组拷贝数扩增区域中检测必需基因的高假阳性率。我们开发了一种名为 CRISPRcleanR 的计算工具，它能够识别和纠正与 CRISPR-Cas9 靶向无关的基因反应。CRISPRcleanR 使用一种无监督的方法，基于对整个基因组中单指导 RNA 折叠变化值的分割，而不假设靶向基因的拷贝数状态。
将我们的方法应用于来自 15 种癌细胞系的现有和新生成的全基因组必需性图谱，我们证明 CRISPRcleanR 在调用必需基因时减少了假阳性，纠正了扩增区域内外的偏差，同时保持了真阳性率。已建立的癌症依赖性和扩增癌症驱动基因的必需性信号在纠正后是可检测的。CRISPRcleanR 报告 sgRNA 折叠变化和归一化读数，因此与下游分析工具兼容，并适用于多种 sgRNA 文库。
CRISPRcleanR 是一种通用的开源工具，用于分析 CRISPR-Cas9 敲除筛选，以识别必需基因。
