Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.9K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.9K
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

89
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
89
Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

152
Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
152

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Dual functional genomics reveals a broad and convergent landscape of asciminib resistance in BCR::ABL1.

Genome medicine·2026
Same author

Ultrasound-Actuated Gene Editing in Human Kidney Organoids.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Interleukin signaling mitigates the inhibitory effects of combined Src/BCR-ABL1 blockade on T-cell activity in Philadelphia chromosome-positive acute lymphoblastic leukemia.

Haematologica·2026
Same author

Characterizing Variants of Uncertain Drug Resistance (VUDRs) Using Quantitative Measurements at Clinical Exposures.

bioRxiv : the preprint server for biology·2025
Same author

Structural Identification of Major Molecular Determinants for Phosphotyrosine Recognition in Tyrosine Kinases Reveals Tumour Promoting and Suppressive Functions.

bioRxiv : the preprint server for biology·2025
Same author

Do the benefits of IDH mutations in high-grade glioma persist beyond the first recurrence? A multi-institutional retrospective analysis.

Journal of neuro-oncology·2025

Related Experiment Video

Updated: Sep 13, 2025

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors
09:22

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

5.6K

A side-by-side comparison of variant function measurements using deep mutational scanning and base editing.

Ivan Sokirniy1, Haider Inam1,2, Marta Tomaszkiewicz1,2

  • 1Huck Institute for the Life Sciences, University Park, PA 16802, United States.

Nucleic Acids Research
|July 31, 2025
PubMed
Summary

CRISPR base editing (BE) effectively annotates gene variants, correlating well with deep mutational scanning (DMS). Simple filters on base editing screens can accurately identify variant function, reducing the need for extensive validation.

More Related Videos

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.1K
Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
06:59

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

2.5K

Related Experiment Videos

Last Updated: Sep 13, 2025

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors
09:22

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

5.6K
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.1K
Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
06:59

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

2.5K

Area of Science:

  • Mammalian functional genomics
  • CRISPR base editing applications
  • High-throughput screening methodologies

Background:

  • Variant annotation is critical for understanding gene function in mammals.
  • Deep mutational scanning (DMS) using cDNA libraries is a standard method.
  • CRISPR base editing (BE) offers a promising alternative for variant annotation.

Purpose of the Study:

  • To directly compare CRISPR base editing (BE) with cDNA deep mutational scanning (DMS) for variant annotation.
  • To assess the reliability of high-throughput BE for annotating variant function.
  • To determine the necessary extent of downstream experimental validation for BE screens.

Main Methods:

  • Direct comparison of cDNA DMS and BE in the same laboratory and cell line.
  • Analysis of short guide RNA (sgRNA) depletion/enrichment based on predicted edits within the sgRNA's 'editing window'.
  • Application of filters for single and multiple edits to assess variant annotation accuracy.

Main Results:

  • High correlation observed between base editor data and gold-standard DMS data.
  • Predicted edits within the sgRNA window significantly improve agreement between DMS and BE.
  • A simple filter for sgRNAs with single edits in their window can annotate a large proportion of variants.
  • Measuring edits in medium-sized validation pools recovers high-quality data for multi-edit guides.

Conclusions:

  • CRISPR base editing screens show a high degree of correlation with DMS, validating its utility for variant annotation.
  • Simple filtering strategies can enable direct variant annotation from BE screens, potentially reducing validation needs.
  • The primary measurable variable in base editor screens is the intended base edits, supporting their functional relevance.