Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Nucleic Acids Res. 2023 Feb 28;51(4):1637-1651. doi: 10.1093/nar/gkad046.
It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, in addition to library-specific false negatives. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared to false negatives. Cumulative analyses across tissues improves our understanding of core essential genes and suggest only a small number of lineage-specific essential genes, enriched for transcription factors that define pathways of tissue differentiation. To recover false negatives, we introduce a method, Joint Log Odds of Essentiality (JLOE), which builds on our prior work with BAGEL to selectively rescue the false negatives without an increased false discovery rate.
人们普遍认为，与之前的技术相比，汇集的文库 CRISPR 敲除筛选在检测导致适应性缺陷的基因方面具有更高的灵敏度和特异性，而这些基因的敲除是鉴定候选癌症靶点的关键步骤。然而，CRISPR 筛选是否饱和的假设在很大程度上尚未得到验证。通过对癌症依赖图谱生成的癌细胞系中的筛选数据进行综合分析，我们表明，典型的 CRISPR 筛选除了文库特异性的假阴性外，还有约 20%的假阴性率。随着基因表达的降低，可重复性急剧下降，而组织内的癌症亚型特异性基因与假阴性相比表现出不同的特征。跨组织的累积分析提高了我们对核心必需基因的理解，并表明只有少数谱系特异性必需基因富集了定义组织分化途径的转录因子。为了恢复假阴性，我们引入了一种方法，即联合必需性对数似然比（JLOE），该方法基于我们之前与 BAGEL 的合作，选择性地挽救假阴性，而不会增加假发现率。
