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Genome-wide single-cell perturbation screens with VIPerturb-seq
Alexandra Bradu1,2, John D Blair1,2, Isabella N Grabski1,2
1New York Genome Center, New York, NY.
Biorxiv : the Preprint Server for Biology
|February 23, 2026
Summary
VIPerturb-seq enhances CRISPR screening with single-cell sequencing for genome-wide genetic perturbation mapping. This scalable platform improves throughput and efficiency for molecular phenotype analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- CRISPR screening coupled with single-cell sequencing (Perturb-seq) maps genetic perturbations to molecular phenotypes.
- Current Perturb-seq methods face cost and throughput limitations for genome-wide screens.
Purpose of the Study:
- Introduce VIPerturb-seq, a platform for routine, cost-effective, genome-wide Perturb-seq.
- Enhance scalability and efficiency of large-scale genetic screens.
Main Methods:
- Developed a split probe strategy for detecting genome-wide CRISPR libraries in fixed cells.
- Integrated optional phenotypic enrichment for Very Important Perturbations (VIP).
- Enabled combinatorial indexing for a 50-fold increase in Perturb-seq throughput.
Main Results:
- Demonstrated VIPerturb-seq using the genome-wide CRISPRi library (GuEST-List).
- Successfully conducted both unbiased and phenotypically enriched genome-wide screens.
- Validated the sensitivity, scalability, and efficiency of the VIPerturb-seq platform.
Conclusions:
- VIPerturb-seq facilitates routine genome-wide Perturb-seq experiments.
- The platform supports both targeted research and large-scale data generation for virtual cell construction.
- VIPerturb-seq significantly advances the capacity for comprehensive genetic perturbation analysis.
