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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...
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...
Hardy-Weinberg Principle01:49

Hardy-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.
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
Frequency-dependent Selection01:21

Frequency-dependent Selection

When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.

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Related Experiment Video

Updated: May 28, 2026

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
08:27

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

Stability selection for genome-wide association.

David H Alexander1, Kenneth Lange

  • 1Department of Biomathematics, UCLA, Los Angeles, California 90095-1766, USA. dalexander@ucla.edu

Genetic Epidemiology
|October 20, 2011
PubMed
Summary
This summary is machine-generated.

Stability selection for genome-wide association studies effectively controls error rates but can lack power due to SNP correlations. Grouping SNPs improves region identification but remains less powerful than simpler methods.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Area of Science:

  • Genetics
  • Statistical genetics
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) aim to identify genetic variants associated with diseases.
  • Variable selection is crucial for identifying true associations within high-dimensional GWAS data.
  • Existing methods may struggle with the complex correlation structures inherent in genetic data.

Purpose of the Study:

  • To evaluate the efficacy of the "stability selection" procedure for variable selection in GWAS.
  • To assess if stability selection can identify novel significant regions or challenge existing findings.
  • To investigate the impact of linkage disequilibrium on stability selection performance.

Main Methods:

  • Application of the Meinshausen and Bühlmann stability selection procedure to seven GWAS datasets.
  • Analysis of stability selection's performance in controlling family-wise error rate (FWER).
  • Modification of the procedure by aggregating single nucleotide polymorphism (SNP) markers into groups.

Main Results:

  • Stability selection demonstrated effective control of the family-wise error rate.
  • The procedure exhibited a loss of statistical power, particularly with individual SNPs, due to linkage disequilibrium.
  • Aggregating nearby SNPs into groups improved the identification of important GWAS regions.
  • The modified group-based approach still showed lower power compared to simpler marginal testing methods in simulations.

Conclusions:

  • Stability selection is a viable method for controlling error rates in GWAS.
  • Linkage disequilibrium significantly impacts stability selection, necessitating adjustments for optimal performance.
  • While grouping SNPs enhances region detection, simpler marginal association tests remain more powerful and computationally efficient.