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

FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

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...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

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

Sort by
Same author

Mutation count and mutation profile analyses of single-nucleotide variants in single human colon crypts.

bioRxiv : the preprint server for biology·2026
Same author

RAG-mediated structural variation and its impact on relapse risk in acute lymphoblastic leukemia.

medRxiv : the preprint server for health sciences·2026
Same author

Germline VCF Annotator: a lightweight pipeline for processing germline VCFs with robust variant extraction and read evidence quality control.

bioRxiv : the preprint server for biology·2026
Same author

Fine Structural Features of Complex InDels and NHEJ Repair at Naturally Occurring Damage Sites in Normal Human Colon Crypts.

bioRxiv : the preprint server for biology·2026
Same author

Author Correction: Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia.

Nature immunology·2025
Same author

High-depth Whole Genome Sequencing of Single Human Colon Crypts Uncovers New View on Crypt Clonality.

bioRxiv : the preprint server for biology·2025
Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026
Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026
Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026
Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026
Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026
Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jun 25, 2026

Indel Detection following CRISPR/Cas9 Mutagenesis using High-resolution Melt Analysis in the Mosquito Aedes aegypti
05:30

Indel Detection following CRISPR/Cas9 Mutagenesis using High-resolution Melt Analysis in the Mosquito Aedes aegypti

Published on: September 10, 2021

Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes.

Yong Hwee Eddie Loh, Michael R Lieber, Chih-Lin Hsieh

    Biorxiv : the Preprint Server for Biology
    |June 24, 2026
    PubMed
    Summary
    This summary is machine-generated.

    Complex indels, often from DNA double-strand breaks (DSB), are challenging to analyze. FreeBayes most accurately represented these complex variants, enabling better analysis of DNA repair events.

    More Related Videos

    Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations
    05:51

    Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations

    Published on: June 28, 2021

    A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia
    05:51

    A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

    Published on: June 15, 2011

    Related Experiment Videos

    Last Updated: Jun 25, 2026

    Indel Detection following CRISPR/Cas9 Mutagenesis using High-resolution Melt Analysis in the Mosquito Aedes aegypti
    05:30

    Indel Detection following CRISPR/Cas9 Mutagenesis using High-resolution Melt Analysis in the Mosquito Aedes aegypti

    Published on: September 10, 2021

    Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations
    05:51

    Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations

    Published on: June 28, 2021

    A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia
    05:51

    A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

    Published on: June 15, 2011

    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Complex indels involve both deletions and insertions, often near boundaries.
    • These variants frequently result from double-strand breaks (DSB) repaired by nonhomologous DNA end joining (NHEJ).
    • Existing indel callers struggle with complex indel representation in VCF files.

    Purpose of the Study:

    • To evaluate the performance of different variant calling approaches in representing complex indels.
    • To develop a workflow for analyzing complex indels derived from DSB repair.

    Main Methods:

    • Tested six variant calling pipelines: FreeBayes, HaplotypeCaller, Mutect2, Strelka2, DRAGEN Germline, and DRAGEN Somatic.
    • Simulated complex indels to assess variant representation.
    • Developed a parsing workflow for FreeBayes VCF output.

    Main Results:

    • FreeBayes demonstrated the most consistent representation of simulated complex indels as single variant records.
    • The developed parsing workflow effectively derives deleted and inserted sequences.
    • The approach aids in analyzing DSB repair events in human colon crypts.

    Conclusions:

    • FreeBayes offers superior representation of complex indels compared to other tested callers.
    • A novel parsing workflow enhances the analysis of complex indels.
    • This methodology facilitates the study of endogenous DSB repair mechanisms.