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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

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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.
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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...
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Related Experiment Video

Updated: Mar 26, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Post-GWAS methodologies for localisation of functional non-coding variants: ANGPTL3.

Federico Oldoni1, Jutta Palmen2, Claudia Giambartolomei3

  • 1Department of Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK; Department of Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

Atherosclerosis
|January 23, 2016
PubMed
Summary

Researchers identified a specific genetic variant (rs10889352) influencing angiopoietin-like 3 (ANGPTL3) gene expression and lipid levels, crucial for understanding coronary artery disease risk.

Keywords:
ANGPTL3ChromatinFAIREFunctional polymorphismGenome-wideLDL-CPolymorphismRegulation

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Area of Science:

  • Genetics
  • Molecular Biology
  • Cardiovascular Disease Research

Background:

  • Genome-wide association studies (GWAS) link non-coding ANGPTL3 gene variants to coronary artery disease (CAD) and lipid levels.
  • Linkage disequilibrium at the ANGPTL3 locus complicates identification of causal variants.

Purpose of the Study:

  • To identify functional non-coding variants impacting the ANGPTL3 regulome and their association with CAD risk factors.
  • To investigate the regulatory mechanisms underlying ANGPTL3 expression and lipid metabolism.

Main Methods:

  • Integration of ENCODE regulatory annotations with functional assays (allele-specific formaldehyde-assisted isolation of regulatory elements, electrophoretic mobility shift assay, luciferase reporter assays).
  • Statistical analyses including expression quantitative trait loci (eQTL) and lipid colocalization.
  • Examination of 253 variants associated with ANGPTL3 mRNA expression and/or lipid traits.

Main Results:

  • Identified 46 potentially functional variants within liver regulatory elements.
  • rs10889352 demonstrated allele-specific effects on DNA-protein interactions, reporter gene expression, and chromatin accessibility.
  • These effects correlated with altered low-density lipoprotein cholesterol (LDL-C) levels and ANGPTL3 mRNA expression.

Conclusions:

  • The study successfully localized a functional non-coding variant (rs10889352) affecting ANGPTL3 regulation and lipid metabolism.
  • This variant, located within non-coding regions of DOCK7, suggests complex long-range regulatory effects on ANGPTL3 gene expression.
  • The findings provide a model for analyzing regulatory variants identified through GWAS.