Related Experiment Video
Updated: Jul 6, 2026
13:55
Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization
Published on: February 3, 2013
Does strong linkage disequilibrium guarantee redundant association results?
Dahlia M Nielsen1, Sunil Suchindran, Christopher P Smith
1Program in Statistical Genetics, Department of Genetics, North Carolina State University, Raleigh, NC 27695-7566, USA. dahlia@statgen.ncsu.edu
Genetic Epidemiology
|April 9, 2008
Summary
Tag single nucleotide polymorphisms (SNPs) can act as proxies for other markers, potentially reducing genotyping costs. However, their effectiveness in association studies is compromised when genetic association exists, reducing overall study power.
Area of Science:
- Genetics
- Statistical Genetics
- Bioinformatics
Background:
- Tag single nucleotide polymorphisms (SNPs) are used as proxies for other polymorphic sites due to linkage disequilibrium (LD).
- The assumption is that tag SNPs capture substantial genetic variation, potentially reducing genotyping costs in association studies without power loss.
Purpose of the Study:
- To directly examine the assumption that strong LD between markers implies high correlation between association test results.
- To evaluate the reliability of tag SNPs as proxies for other markers in genetic association studies.
Main Methods:
- Analysis of the relationship between linkage disequilibrium (LD) and correlation of association test outcomes.
- Examination under both null hypothesis (no association) and alternative hypothesis (genetic association exists) scenarios.
Main Results:
- Under the null hypothesis, the relationship between LD and association test outcome correlation is clear but not always ideal.
- Under the alternative hypothesis, high LD does not guarantee that one marker's association test result is a direct substitute for another's.
Conclusions:
- The use of tag SNPs as proxies may not be reliable when genetic association is present in a region.
- Eliminating markers in favor of tag SNPs can lead to a reduction in the overall power of association studies.
Related Concept Videos
01:18Dihybrid Crosses
Overview
01:49Hardy-Weinberg Principle
Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...
02:03Law of Independent Assortment
While Mendel’s Law of Segregation states that the two alleles for one gene are separated into different gametes, a different question of how different genes are inherited remains. For example, is the gene for tall plants inherited with the gene for green peas? Mendel asked this question by experimenting with a dihybrid cross; a cross in which both parents are homozygous for two distinct traits resulting in an F1 generation that are heterozygous for both traits.
02:03Law of Independent Assortment
While Mendel’s Law of Segregation states that the two alleles for one gene are separated into different gametes, a different question of how different genes are inherited remains. For example, is the gene for tall plants inherited with the gene for green peas? Mendel asked this question by experimenting with a dihybrid cross; a cross in which both parents are homozygous for two distinct traits resulting in an F1 generation that are heterozygous for both traits.
00:49Ligand Binding and Linkage
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
00:49Ligand Binding and Linkage
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...