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CRISPR

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced Short...

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

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Related Experiment Video

Updated: Jun 24, 2026

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

Published on: February 26, 2019

Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs.

Furkan Özden¹, Peter Minary¹

¹Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK.

Nucleic Acids Research

|September 14, 2024

Summary

CRISPR genome editing faces challenges with off-target effects. crispAI predicts uncertainty in off-target activity and offers a genome-wide sgRNA efficiency score for better risk assessment in genetic manipulation.

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Last Updated: Jun 24, 2026

Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution

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Published on: February 26, 2019

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Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

CRISPR-based genome editing offers precise genetic manipulation but is limited by off-target effects.
Current prediction methods focus on point estimates, not fully capturing risks.
Uncertainty in off-target activity is crucial for clinical applications.

Purpose of the Study:

To develop a novel approach for predicting uncertainty estimates of CRISPR off-target cleavage activity.
To introduce crispAI-aggregate, a genome-wide single guide RNA (sgRNA) efficiency score.
To provide a more comprehensive risk assessment for CRISPR applications.

Main Methods:

Utilized a neural network architecture for predicting uncertainty.
Employed the Zero Inflated Negative Binomial (ZINB) model to capture count noise in off-target data.
Developed crispAI-aggregate for genome-wide sgRNA efficiency scoring.

Main Results:

crispAI provides calibrated uncertainty estimates for off-target cleavage.
The approach demonstrates superior predictive performance over existing methods.
crispAI-aggregate offers richer information for sgRNA prioritization.

Conclusions:

crispAI enhances risk assessment in CRISPR genome editing by quantifying prediction uncertainty.
The developed tool facilitates improved decision-making in sgRNA design.
This work advances the safety and applicability of CRISPR technologies.