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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.
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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
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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,...

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Published on: June 21, 2018

Marker selection for genetic case-control association studies.

Fredrik H Pettersson1, Carl A Anderson, Geraldine M Clarke

  • 1Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. fredrikp@well.ox.ac.uk

Nature Protocols
|April 25, 2009
PubMed
Summary
This summary is machine-generated.

Selecting appropriate genetic markers, such as single nucleotide polymorphisms (SNPs), is crucial for the success of association studies. This protocol outlines strategies for choosing tagSNPs to efficiently detect disease associations.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Association studies are vital for identifying genetic links to diseases.
  • Marker selection strategy significantly impacts the statistical power and reliability of association studies.
  • Single nucleotide polymorphisms (SNPs) are commonly used markers due to their abundance.

Purpose of the Study:

  • To provide guidelines for selecting single nucleotide polymorphisms (SNPs) as genetic markers.
  • To detail strategies for marker selection in candidate gene, regional, and genome-wide association studies.
  • To explain the utility of tagSNPs in capturing linkage disequilibrium (LD) for efficient association studies.

Main Methods:

  • Utilizing publicly available web-based resources for data retrieval and browsing.
  • Employing software like Haploview and Goldsurfer2 for linkage disequilibrium (LD) analysis.
  • Selecting tagSNPs as proxies for correlated SNPs in high LD.

Main Results:

  • Demonstrated methods for selecting tagSNPs in both candidate gene and genome-wide association studies.
  • Provided illustrative examples for SNP selection processes.
  • Highlighted the importance of LD in optimizing marker selection.

Conclusions:

  • Effective tagSNP selection enhances the power and efficiency of genetic association studies.
  • The described protocol offers a practical approach to marker selection for diverse study designs.
  • Leveraging LD information is key to successful and cost-effective genetic association research.