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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: Apr 20, 2026

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.

Aaron A Diaz¹, Han Qin², Miguel Ramalho-Santos³

¹Institute for Human Genetics, University of California, San Francisco, CA, USA The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.

Nucleic Acids Research

|November 28, 2014

Summary

This summary is machine-generated.

HiTSelect is a new analysis pipeline that improves the accuracy of genetic screens. It addresses noise and bias in high-throughput data from RNAi and CRISPR screens, enabling better identification of functional genes and pathways.

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Last Updated: Apr 20, 2026

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

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Published on: September 4, 2019

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

High-throughput genetic screens using synthetic oligonucleotides and next-generation sequencing enable large-scale gene knockdown and knockout studies.
Interpretation of this complex data is challenging due to random noise and statistical biases.

Purpose of the Study:

To develop a robust analysis pipeline, HiTSelect, for accurate identification of screen hits from genetic screens.
To address off-target effects, gene silencing efficiency variance, and sequencing depth variations.

Main Methods:

Developed HiTSelect, a comprehensive bioinformatics pipeline for genetic screen data analysis.
Incorporated methods to control for technical variability and integrate metadata.
Validated HiTSelect using genome-wide RNAi and CRISPR/Cas9 screening data.

Main Results:

HiTSelect demonstrated superior performance in analyzing genetic screen data.
The pipeline effectively identifies functionally relevant genes and pathways.
Successfully addressed common sources of noise and bias in high-throughput screening.

Conclusions:

HiTSelect provides a rigorous approach for analyzing large-scale genetic screens.
The open-source package facilitates accurate hit selection and pathway discovery.
Enables more reliable interpretation of RNAi and CRISPR/Cas9 screening results.