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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

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Published on: February 21, 2015

Visualization of genomic aberrations using Affymetrix SNP arrays.

André Müller1, Karlheinz Holzmann, Hans A Kestler

  • 1Internal Medicine I, University of Ulm, D-89069 Ulm, Germany.

Bioinformatics (Oxford, England)
|December 2, 2006
PubMed
Summary

This study introduces IdeogramBrowser, a novel open-source software for visualizing DNA copy number aberrations detected by high-density SNP microarrays. It aids in exploring large cancer datasets by interactive karyotypic representation and gene linkage.

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Last Updated: Jul 18, 2026

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • DNA copy number aberrations are common in cancer.
  • Microarray technologies, especially high-density single nucleotide polymorphism (SNP) arrays, offer high resolution for detecting these aberrations.
  • Analyzing the vast data generated by these arrays presents a significant challenge.

Purpose of the Study:

  • To introduce IdeogramBrowser, a new open-source software tool.
  • To provide an interactive karyotypic visualization for multiple aberration profiles from SNP array data.
  • To facilitate the exploration of large cancer genomic datasets by linking aberration regions to gene information.

Main Methods:

  • Development of IdeogramBrowser, a platform-independent Java application.
  • Designed for use with Affymetrix SNP arrays.
  • Incorporates interactive karyotypic visualization and direct links to GeneCards for gene representation.

Main Results:

  • IdeogramBrowser enables interactive visualization of DNA copy number aberrations.
  • The software facilitates the assessment of consensus aberration regions.
  • Direct links to GeneCards enhance the understanding of affected genes.

Conclusions:

  • IdeogramBrowser is a valuable open-source tool for analyzing high-density SNP array data in cancer research.
  • Its visualization capabilities aid in the explorative assessment of genomic aberrations.
  • The software simplifies the interpretation of complex genomic data by integrating aberration profiles with gene information.