CRISPR Screening for Drug Development

CRISPR KO (knockout) uses Cas9 to create permanent DNA double-strand breaks, resulting in gene knockout through NHEJ-mediated indels. This provides maximal phenotypic effect and is ideal for loss-of-function studies.

CRISPRi (interference) uses catalytically dead Cas9 (dCas9) fused to the KRAB transcriptional repression domain to block transcription without modifying DNA. This is reversible and suitable for studying essential genes or dose-dependent effects.

CRISPRa (activation) uses dCas9 fused to transcriptional activators (VP64, p65, HSF1) to upregulate gene expression from the endogenous locus. This enables gain-of-function screens and studies of resistance mechanisms.

Our standard whole-genome libraries include 4-6 sgRNAs per gene, which are algorithmically selected for high on-target activity and low off-target predictions. This redundancy ensures robust hit calling and allows identification of false positives through cross-validation of multiple guides targeting the same gene.

We offer 50+ pre-validated cell lines optimized for lentiviral transduction and CRISPR screening. These include commonly used cancer cell lines (HeLa, A549, MCF-7, etc.) as well as specialty lines. If your cell line of interest is not on our validated list, we can evaluate and optimize it for screening with an additional timeline.

Hit calling is performed using the MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) algorithm, which uses a robust ranking aggregation (RRA) method to identify genes where multiple sgRNAs are consistently enriched or depleted. This approach provides statistically robust hit identification with controlled false discovery rates.

Standard deliverables include: QC metrics (coverage, Gini index, sgRNA counts), MAGeCK analysis results, volcano plots, log-fold change visualizations, KEGG pathway enrichment, Gene Ontology analysis, and a ranked gene hit list. Custom downstream analysis, including integration with public datasets (DepMap) and pathway-specific analysis, is available upon request.

Yes, you can provide your own cell lines. However, we recommend using our pre-validated lines to minimize optimization time. If you need to use a specific cell line, we can evaluate its suitability for screening and optimize transduction conditions, which may require additional time and cost.

We support both pooled and arrayed screening formats. Pooled screens are ideal for whole-genome or large library screens with selection-based readouts (drug resistance, cell viability). Arrayed screens using multi-well formats are suitable for targeted libraries with high-content phenotypic analysis (imaging, FACS).