Recovering False Negatives in CRISPR Fitness Screens With Jloe

Authors

Merve Dede
Traver Hart

Publication Date

2-28-2023

Journal

Nucleic Acids Research

Abstract

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.

Keywords

Humans, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, Gene Library, Genes, Essential, Neoplasms, Cell Line, Tumor, Gene Knockout Techniques

DOI

10.1093/nar/gkad046

PMID

36727483

PMCID

10.1093/nar/gkad046

PubMedCentral® Posted Date

2-2-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes