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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

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...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Genomics02:02

Genomics

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...
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...

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Related Experiment Video

Updated: Jun 11, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

A versatile gene-based test for genome-wide association studies.

Jimmy Z Liu1, Allan F McRae, Dale R Nyholt

  • 1Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia. jimmy.liu@uqconnect.edu.au

American Journal of Human Genetics
|July 6, 2010
PubMed
Summary

We developed a versatile gene-based test for genome-wide association studies (GWAS). This new method, VEGAS, efficiently analyzes various GWAS designs, including family-based and summary data, identifying associated genes with reduced computation time.

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

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Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) are crucial for identifying genetic variants associated with diseases.
  • Existing gene-based tests have limitations in applicability across diverse GWAS designs and computational efficiency.

Purpose of the Study:

  • To develop a versatile and computationally efficient gene-based test for genome-wide association studies (GWAS).
  • To create a method applicable to various GWAS designs, including family-based, meta-analyses, DNA-pooling, and singleton data.

Main Methods:

  • Developed VEGAS (versatile gene-based association study), a novel gene-based test incorporating all markers within a gene.
  • Accounted for linkage disequilibrium using multivariate normal distribution simulations.
  • Implemented the approach in a user-friendly web interface and a downloadable application.

Main Results:

  • VEGAS demonstrated computational efficiency, yielding results equivalent to permutation tests in a fraction of the time for singleton data.
  • Successfully replicated known gene associations for height and melanoma in independent GWAS datasets.
  • Showcased potential for identifying novel associated genes and supporting network-based approaches.

Conclusions:

  • VEGAS offers a versatile, efficient, and broadly applicable gene-based testing framework for GWAS.
  • The method facilitates gene discovery, SNP selection for replication, and pathway analysis.
  • Accessible implementation via web interface and downloadable application promotes wider adoption.