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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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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Single Nucleotide Polymorphisms-SNPs01:05

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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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Genome Copying Errors02:46

Genome Copying Errors

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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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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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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Karyotyping01:17

Karyotyping

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Detection of Copy Number Alterations Using Single Cell Sequencing
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VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism.

HyoYoung Kim1, Samsun Sung2, Seoae Cho2

  • 1Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea.

Asian-Australasian Journal of Animal Sciences
|November 1, 2014
PubMed
Summary
This summary is machine-generated.

Copy number variation (CNV) and single nucleotide polymorphism (SNP) data are valuable genetic resources. A new web-based tool, VCS, visualizes this data, aiding interpretation of complex phenotypes and disease susceptibility.

Keywords:
Copy Number VariationCytomapHomozygositySingle Nucleotide PolymorphismVisualization

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) are crucial genetic resources for understanding complex phenotypes and disease susceptibility.
  • Existing public databases contain numerous CNVs and SNPs, but their direct analysis is challenging without effective visualization tools.

Purpose of the Study:

  • To develop a user-friendly, web-based tool for visualizing detected CNVs and SNPs.
  • To facilitate the interpretation of biological meaning from numerical CNV and SNP data.

Main Methods:

  • Development of a web-based visualization tool named VCS (Visualization of CNV or SNP).
  • Implementation of six distinct visualization modules within the VCS tool.

Main Results:

  • The VCS tool enables intuitive interpretation of complex genetic variation data.
  • Six visualization functions are provided: genome content enrichment in CNVs, physical distribution on chromosomes, log2 ratio distribution, CNV/SNP counts per bin, SNP genotype homozygosity distribution, and gene cytomaps within CNV/SNP regions.

Conclusions:

  • The VCS tool significantly enhances the utility of CNV and SNP data for biological interpretation.
  • This visualization approach aids researchers in understanding genetic contributions to complex traits and diseases.