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

17.7K
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%...
17.7K
Genomics02:02

Genomics

36.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.5K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.3K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.3K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

3.0K
3.0K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

13.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
13.6K

You might also read

Related Articles

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

Sort by
Same author

Transcriptomics of type 1 diabetes progression: a validation study in newly diagnosed patients.

EBioMedicine·2026
Same author

Clarifying the scope and capabilities of ROTS in differential expression analysis.

Bioinformatics (Oxford, England)·2026
Same author

Joint modeling of longitudinal and time-to-event data for dynamic disease risk prediction using proteomics.

Protein science : a publication of the Protein Society·2026
Same author

REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research.

Bioinformatics (Oxford, England)·2026
Same author

Therapeutic TG2 inhibition reverses systemic multiomic dysregulation in celiac disease.

BMC medicine·2026
Same author

Testosterone Exposure During Fetal Masculinization Programming Window Determines the Kidney Size in Adult Mice.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·2026

Related Experiment Video

Updated: Jul 19, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.6K

VarSCAT: A computational tool for sequence context annotations of genomic variants.

Ning Wang1,2, Sofia Khan1, Laura L Elo1,2,3

  • 1Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.

Plos Computational Biology
|August 11, 2023
PubMed
Summary

The Variant Sequence Context Annotation Tool (VarSCAT) addresses limitations in analyzing genomic variant sequence contexts. VarSCAT offers versatile annotation for tandem repeats and insertions/deletions, improving variant interpretation.

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

33.8K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.2K

Related Experiment Videos

Last Updated: Jul 19, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.6K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

33.8K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.2K

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genomic variant sequence contexts are crucial for biological interpretation and variant calling.
  • Existing methods for annotating diverse sequence contexts, like tandem repeats and ambiguous breakpoints, are limited.

Purpose of the Study:

  • To introduce the Variant Sequence Context Annotation Tool (VarSCAT) for comprehensive genomic variant annotation.
  • To provide a versatile and customizable solution for analyzing variant sequence contexts, including tandem repeats and indels.

Main Methods:

  • Development of VarSCAT, a tool for annotating genomic variant sequence contexts.
  • Annotation of human variant sets to assess breakpoint ambiguities and variant characteristics in tandem repeat regions.

Main Results:

  • VarSCAT demonstrates greater versatility and customizability compared to existing methods for STR and indel annotation.
  • Over 75% of human germline and clinically relevant indels exhibit breakpoint ambiguities.
  • More than 80% of human germline small variants in STR regions are indels, with sizes correlating to STR motif sizes.

Conclusions:

  • VarSCAT enhances the analysis of genomic variants, particularly in complex regions like STRs and those with ambiguous breakpoints.
  • The findings highlight the prevalence of breakpoint ambiguities and indel characteristics in human germline variants within STR regions.