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

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Epistasis Analysis01:09

Epistasis Analysis

Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

You might also read

Related Articles

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

Sort by
Same author

Pomegranate Peel Extract Alleviates Psoriasis-like Skin Lesions in Mice Through the Suppression of AhR-Activating Th17/IL-17 Axis and Neuronal-Related Pathways.

International journal of molecular sciences·2026
Same author

Large-scale analysis of temporal gene expression variation in peripheral blood.

Nature communications·2026
Same author

Fabrication and evaluation of a peptide-magnesium bifunctional coating on 3D printed porous tantalum scaffolds for enhanced bone regeneration.

Colloids and surfaces. B, Biointerfaces·2026
Same author

Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.

Genome research·2026
Same author

Functional assessment of a convergent gene network underlying allergic diseases and IgE.

The Journal of allergy and clinical immunology·2026
Same author

A biological-systems-based analysis using proteomic and metabolic network inference reveals mechanistic insights into hepatic steatosis.

Metabolism: clinical and experimental·2026

Related Experiment Video

Updated: May 21, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Genotype-based test in mapping cis-regulatory variants from allele-specific expression data.

Jean Francois Lefebvre1, Emilio Vello, Bing Ge

  • 1Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.

Plos One
|June 12, 2012
PubMed
Summary

A new genotype-based mapping test accurately identifies gene regulatory regions and causal variants by analyzing allelic imbalance (AI) without requiring haplotype information, improving genetic disease and adaptation studies.

More Related Videos

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

Related Experiment Videos

Last Updated: May 21, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

Area of Science:

  • Genetics
  • Evolutionary Biology
  • Medical Genetics

Background:

  • Gene regulatory variation significantly impacts human adaptation and genetic diseases.
  • Allelic imbalance (AI) reveals regulatory variation in cis but existing methods rely on haplotype phasing, which can introduce errors.
  • Accurate identification of regulatory variants is crucial for understanding genetic diversity and disease.

Purpose of the Study:

  • To introduce a novel genotype-based mapping test for regulatory regions that bypasses the need for haplotype inference.
  • To evaluate the performance of this new test against existing haplotype-based methods.
  • To improve the identification of cis-regulatory variants, especially those located farther from their regulated transcripts.

Main Methods:

  • Developed a genotype-based mapping test utilizing a 2x3 contingency table for individuals with and without allelic imbalance (AI).
  • Assessed the test's ability to detect linkage disequilibrium (LD) between regulatory sites and SNPs.
  • Validated the test using simulated datasets and empirical data from genome-wide arrays and RNA sequencing.

Main Results:

  • The genotype-based test demonstrated superior performance compared to haplotype-based tests, particularly as the distance between the regulatory region and transcript increased.
  • The test performed effectively on both simulated and real-world allelic imbalance (AI) datasets.
  • The method successfully identified regulatory regions and potential causal variants without requiring haplotype phasing.

Conclusions:

  • The genotype-based mapping test offers a robust alternative for identifying regulatory regions and variants, especially in population samples with unknown haplotype structures.
  • This approach simplifies the analysis of allelic imbalance (AI) and enhances the discovery of distant cis-regulatory variants.
  • The findings have significant implications for evolutionary and medical genetics research.