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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.
GWAS does not require the identification of the target gene involved in...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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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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Significance testing is a set of statistical methods used to test whether a claim about a parameter is valid. In analytical chemistry, significance testing is used primarily to determine whether the difference between two values comes from determinate or random errors. The effect of a particular change in the measurement protocol, analyst, or sample itself can cause a deviation from the expected result. In the case of a suspected deviation/outlier, we need to be able to confirm mathematically...
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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.
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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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A novel association test for rare variants based on algebraic statistics.

Jingbo Meng1, Wensheng Zhu1, Canhui Li1

  • 1Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China.

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|March 6, 2020
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Summary

This study introduces a new statistical method to analyze rare genetic variants in genome-wide association studies (GWAS). The novel approach improves the detection of associations between rare variants and diseases like coronary artery disease.

Keywords:
Association analysisContingency tablesMarkov Chain Monte CarloMarkov bases

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Area of Science:

  • Genetics
  • Statistical genetics
  • Bioinformatics

Background:

  • Next-generation sequencing has increased the availability of rare variants in the human genome.
  • Genome-wide association studies (GWAS) are increasingly focusing on rare variants.
  • Existing methods for rare variant association testing have limitations, especially with low mutation rates.

Purpose of the Study:

  • To develop a novel statistical method for testing associations between rare variants and discrete phenotypes.
  • To address the challenges posed by the sparsity of data in contingency tables for rare variants.
  • To improve the power of association tests for rare variants in GWAS.

Main Methods:

  • Proposed a novel association test generalizing Fisher's exact test.
  • Utilized the multivariate hypergeometric distribution within algebraic statistics.
  • Computed exact p-values for the proposed test.

Main Results:

  • The proposed method demonstrated superior performance compared to existing methods in simulations.
  • The method showed effectiveness even with heterogeneity among causal variants.
  • Successfully applied to real-world genetic association studies for coronary artery disease and hypertension.

Conclusions:

  • The novel generalized Fisher's exact test provides a powerful tool for rare variant association analysis.
  • The method is robust and applicable to complex genetic studies.
  • Offers an advancement in the statistical toolkit for GWAS involving rare variants.