GO-CRISPR: a highly controlled workflow to improve discovery of gene essentiality

Genome-wide CRISPR screens aid researchers in discovering genes that function across a broad range of cellular mechanisms. Loss-of-function screens are particularly useful for identifying essential genes through loss of cell fitness measurements. However, loss-of-function screens are more challenging compared to gain-of-function screens due to the limited dynamic range of decreased sgRNA sequence detection. Here we describe Guide-Only control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, Toolset for the Ranked Analysis of GO-CRISPR Screens (TRACS; https://github.com/developerpiru/TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer. We compare the results from our GO-CRISPR screen and demonstrate the discovery of novel pathways that were not possible using the currently established CRISPR screening method. GO-CRISPR and its accompanying software, TRACS, robustly improve the discovery of essential genes in challenging biological scenarios.