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Related Concept Videos

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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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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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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Related Experiment Video

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Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
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Mapsnp: an R package to plot a genomic map for single nucleotide polymorphisms.

Fuquan Zhang1, Yong Xu2, Hongbao Cao3

  • 1Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China; Unit on Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America.

Plos One
|April 9, 2015
PubMed
Summary

Single-nucleotide polymorphisms (SNPs) are key genetic variations. The new "mapsnp" R package provides an easy way to visualize SNP genomic locations and their relationship to genes and transcripts.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Single-nucleotide polymorphisms (SNPs) represent common genetic variations crucial for association studies.
  • Understanding SNP function requires visualizing their genomic context, including physical location relative to genes and transcript structures.
  • Existing tools for such visualizations are limited, hindering intuitive interpretation.

Purpose of the Study:

  • To develop a user-friendly R package for visualizing SNP genomic data.
  • To integrate chromosome ideograms, genomic coordinates, and SNP information into a comprehensive map.
  • To facilitate the understanding of SNP functions through enhanced visualization.

Main Methods:

  • Development of the "mapsnp" R package.
  • Implementation of functions to plot genomic maps for selected SNPs.
  • Integration of chromosome ideograms, SNP coordinates, and transcript structures.

Main Results:

  • The "mapsnp" package provides a flexible tool for generating genomic maps of SNPs.
  • Visualizations include relative chromosome location, host gene, and transcript structures.
  • The package integrates SNP locations and labels with genomic context.

Conclusions:

  • "mapsnp" offers a valuable and accessible solution for visualizing SNP data.
  • The package aids in interpreting SNP functions by providing intuitive genomic context.
  • This tool enhances the analysis of genetic variations in genome-wide association studies.