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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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Related Experiment Video

Updated: Apr 28, 2026

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

The one-week automated genome-wide optical pooled screen.

Bryce Kirby¹, Matteo Di Bernardo^2,3, Iain M Cheeseman^2,4

¹Broad Institute of MIT and Harvard; 415 Main St., Cambridge, MA 02142.

Biorxiv : the Preprint Server for Biology

|April 27, 2026

Summary

This summary is machine-generated.

We developed OttoSeq, an automated platform for optical pooled screens (OPS), significantly reducing labor and time. This innovation enables rapid, large-scale genetic screens for biological discovery.

Keywords:

AI-Driven Scientific Discovery CRISPR screening Cell Painting High throughput biology LLM automated annotation automated in situ sequencing high throughput computing optical pooled screening single-cell genomics

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Last Updated: Apr 28, 2026

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

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Published on: September 4, 2019

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Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

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Area of Science:

Genomics
High-content screening
Bioinformatics

Background:

Optical pooled screens (OPS) are powerful for large-scale genetic screens but are limited by complex, labor-intensive protocols for in situ sequencing and data analysis.
Existing methods require significant manual effort and time, hindering the throughput and accessibility of OPS.

Purpose of the Study:

To develop an automated platform, OttoSeq, that integrates fluid handling and data analysis to overcome the bottlenecks in optical pooled screens.
To demonstrate the capability of OttoSeq in performing a genome-wide functional genomics screen efficiently.

Main Methods:

Developed OttoSeq by combining the Otto2 fluid handling system with the Brieflow analysis pipeline for automated OPS.
Executed a genome-wide cell painting screen using OttoSeq, involving the analysis of over 5 million cells across 21,732 gene knockout perturbations.
Utilized automated data processing to interpret functional gene clusters.

Main Results:

Successfully automated the entire OPS workflow, from cell perturbation to data interpretation.
Completed a genome-wide cell painting screen in just eight days, a significant reduction in processing time.
Analyzed over 5 million high-quality cells, providing 224 cells per gene knockout, and identified 320 distinct functional gene clusters.

Conclusions:

OttoSeq represents a major advancement in automating optical pooled screens, making large-scale functional genomics more accessible and efficient.
The platform's speed and capacity enable rapid exploration of cellular functions at a genome-wide scale.
Automated OPS platforms like OttoSeq are crucial for accelerating biological discovery and understanding gene function.