Determining optimal sgRNA coverage and screening duration for pooled CRISPR screens: A quantitative framework

CRISPR-based loss-of-function screening has emerged as a powerful tool for systematically characterizing gene functions. However, standardized quantification metrics for sgRNA coverage-a critical parameter determining genome-wide screening reliability and resource efficiency, remain undefined. In this study, we first conducted systematic sgRNA coverage tests in HeLa cells to determine the optimal coverage for CRISPR^iBAR knockout libraries. Furthermore, we incorporated multiple timepoints to monitor sgRNA-mediated gene knockout dynamics. Here, balancing data quality, time efficiency, and cost, we identify 15 days and 800 × coverage as the optimal screening parameters for standard iBAR‑based CRISPR screens. Data from varying coverage levels can also serve as essential references for screening under different experimental conditions. Longitudinal analysis revealed that extending the screening period beyond 15 days maintains stable sgRNA distribution patterns within the cell population. This study establishes key parameter benchmarks to ensure CRISPR knockout screening efficacy and reproducibility, providing a solid foundation for downstream drug screening and target identification.