Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

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...

What is Variation?

What is Variation?

Apart from the measures of central tendency, distribution, outliers, and the changing characteristics of data with time, an important characteristic of any data set is its variation or spread. In some data sets, the data values are concentrated closely near the mean; in others, the data values are more widely spread out from the mean.
The range, standard deviation, standard error, and variance are the different measures of variation.
Range: The range is the difference between its maximum and...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

Variation

Variation

An important characteristic of any set of data is the variation in the data. In some data sets, the data values are concentrated closely near the mean; in other data sets, the data values are more widely spread out from the mean. The most common measure of variation, or spread, is the standard deviation, which is the square root of variance.
When independent and dependent variables are plotted on a scatter plot, the slope of a line is a value that describes the rate of change between the two...

Variation of Atmospheric Pressure

Variation of Atmospheric Pressure

Change in atmospheric pressure with height is particularly interesting. The decrease in atmospheric pressure with increasing altitude is due to the decreasing gravitational force per unit area as we move away from the surface of the earth.
Assuming the air temperature is constant at a given altitude and that the ideal gas law of thermodynamics describes the atmosphere to a good approximation, one can find the variation of atmospheric pressure with height.
Let p(y) be the atmospheric pressure at...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

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%...

You might also read

Related Articles

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

Sort by

Same author

Inferring and evaluating network medicine-based disease modules with nextflow.

Bioinformatics (Oxford, England)·2026

Same author

Aberrant splicing in human cancer shows possible functional impact on transcription factors.

Oncogene·2026

Same author

An Integrated Skin Cell Atlas Decodes the Pilosebaceous Unit.

The Journal of investigative dermatology·2026

Same author

Phenotypic similarity of adverse drug reactions and disease phenotypes is a bridge to mechanistic discovery.

npj drug discovery·2026

Same author

Family-Based Study Reveals <i>PDE11A/PDE11A-AS1</i> Variants in Testicular Germ Cell Tumor Predisposition.

International journal of molecular sciences·2026

Same author

Origin of sexual dimorphism in osteoarthritis risk: the impact of pregnancy and parental care.

BMC public health·2026

Search research articles

Related Experiment Video

Updated: Feb 10, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

CoNVaQ: a web tool for copy number variation-based association studies.

Simon Jonas Larsen¹, Luisa Matos do Canto², Silvia Regina Rogatto³

¹Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense, DK-5230, DK, Denmark. sjlarsen@imada.sdu.dk.

|May 20, 2018

Summary

CoNVaQ is a new web tool for copy number variation (CNV) association studies. It helps researchers easily find genomic regions linked to diseases using CNV data.

Keywords:

Association studies Copy number variation

More Related Videos

Shuttle Box Assay as an Associative Learning Tool for Cognitive Assessment in Learning and Memory Studies using Adult Zebrafish

Shuttle Box Assay as an Associative Learning Tool for Cognitive Assessment in Learning and Memory Studies using Adult Zebrafish

Published on: July 12, 2021

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems

Published on: February 6, 2018

Related Experiment Videos

Last Updated: Feb 10, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Shuttle Box Assay as an Associative Learning Tool for Cognitive Assessment in Learning and Memory Studies using Adult Zebrafish

Shuttle Box Assay as an Associative Learning Tool for Cognitive Assessment in Learning and Memory Studies using Adult Zebrafish

Published on: July 12, 2021

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems

Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems

Published on: February 6, 2018

Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

Copy number variations (CNVs) are genomic alterations linked to complex diseases.
Genome-Wide Association Studies (GWAS) extended to CNVs identify structural variants associated with human traits.

Purpose of the Study:

To present CoNVaQ, a user-friendly web-based tool for CNV association studies.
To enable biologists and clinicians to perform CNV data analysis without software installation.

Main Methods:

CoNVaQ utilizes two models: Fisher's exact test and a novel query-based model.
It computes global q-value statistics through repeated sample permutations.
The platform analyzes CNV segments to identify associations with phenotypes.

Main Results:

CoNVaQ facilitates the discovery of genomic regions with significant CNV associations.
The tool was demonstrated using a dataset of HPV-positive and HPV-negative penile cancer patients.
Analysis of results can identify overrepresented Gene Ontology (GO) terms and pathways.

Conclusions:

CoNVaQ offers a simplified workflow for CNV association studies via a web platform.
It empowers researchers without requiring software installation.
The tool is also available as an R package and accessible at https://convaq.compbio.sdu.dk.