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Genetic Screens

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...

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Updated: Oct 6, 2025

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

Pooled genetic perturbation screens with image-based phenotypes.

David Feldman^1,2, Luke Funk^1,3, Anna Le^1,4

¹Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Nature Protocols

|January 13, 2022

Summary

This summary is machine-generated.

Optical pooled screens enable large-scale genetic screens by integrating CRISPR perturbations with high-content imaging and in situ sequencing for precise genotype and phenotype analysis.

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Area of Science:

Cell Biology
Genetics
Bioengineering

Background:

Microscopy is crucial for cell biology but lacks high-throughput sequencing for large-scale genetic screens.
Efficient genetic engineering combined with high-resolution phenotypic readouts accelerates discovery of genetic components.

Purpose of the Study:

To develop a method for integrating genetic perturbations with high-content imaging for scalable genetic screening.
To enable high-throughput, single-cell resolution of both phenotype and genotype in genetic screens.

Main Methods:

Utilizing optical pooled screens with in situ sequencing and barcoded lentiviral libraries (e.g., CRISPR).
Employing standard lentiviral vectors and molecular biology techniques for genetic perturbation.
Implementing an automated image analysis pipeline for parallel sequencing analysis.

Main Results:

Achieved massively scalable integration of genetic perturbations with high-content imaging assays.
Provided single-cell resolution of phenotype and engineered genotype.
Demonstrated scalability to millions of cells with accurate sequencing for >10^6 perturbations.

Conclusions:

Optical pooled screens with in situ sequencing overcome limitations of traditional microscopy for large-scale genetic screens.
This method facilitates the discovery of genetic components underlying biological processes and diseases.
The protocol is scalable, accurate, and integrates genetic engineering with detailed phenotypic analysis.