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Related Concept Videos

Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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Comparing Copy Number Variations and SNPs02:26

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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Incomplete Dominance01:43

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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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Principles of Pharmacogenetics: Types of Genetic Variants01:27

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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...
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Law of Independent Assortment02:03

Law of Independent Assortment

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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.
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Related Experiment Video

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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

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Are rare variants really independent?

Asuman Turkmen1,2, Shili Lin1

  • 1Department of Statistics, The Ohio State University, Columbus, Ohio, United States of America.

Genetic Epidemiology
|March 17, 2017
PubMed
Summary
This summary is machine-generated.

Commonly used linkage disequilibrium (LD) measures fail to detect associations involving rare variants. A new method, polychoric correlation, shows promise for analyzing rare variant data in genetic association studies.

Keywords:
1000 Genomes dataGWASlinkage disequilibriumnext-generation sequencing datapolychoric correlation

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • High-density genotyping provides access to rare genomic variants.
  • Linkage disequilibrium (LD) is crucial for evolutionary insights and association mapping.
  • Understanding LD structure, especially for rare variants, is vital for improving association study power.

Purpose of the Study:

  • To evaluate the effectiveness of common LD measures with rare variants.
  • To address limitations in detecting LD involving rare variants.
  • To propose and validate an alternative LD measure for rare variant analysis.

Main Methods:

  • Assessed performance of two standard LD measures with rare variants.
  • Identified computational and theoretical limitations of existing LD measures.
  • Proposed and applied polychoric correlation as an alternative LD measure.
  • Validated findings using simulated data and the 1000 Genomes dataset.

Main Results:

  • Standard LD measures are inadequate for detecting LD with rare variants.
  • Rare variants often incorrectly assumed to be independent in association tests.
  • Polychoric correlation demonstrates capability in detecting LD involving rare variants.
  • Performance analysis highlights implications for rare variant association studies.

Conclusions:

  • Existing LD measures require re-evaluation for studies involving rare variants.
  • Polychoric correlation offers a viable alternative for LD analysis with rare variants.
  • Improved LD assessment can enhance the power and accuracy of genetic association studies for rare variants.