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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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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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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...
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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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Related Experiment Video

Updated: Sep 6, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing
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DECoN: A Detection and Visualization Tool for Exonic Copy Number Variants.

Anna Fowler1

  • 1Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK. A.Fowler@liverpool.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|June 25, 2022
PubMed
Summary

DECoN is a new software tool that detects copy number variants (CNVs) affecting whole exons using read depth changes. It is optimized for clinical use, aiding in the identification of CNVs from targeted sequencing data.

Keywords:
BioinformaticsCopy number variantsSequencingTargeted panelsWhole exome

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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Detecting copy number variants (CNVs) from targeted sequencing, including whole-exome sequencing, is challenging.
  • CNV breakpoints are not always captured, complicating variant identification.

Purpose of the Study:

  • To introduce DECoN, a novel software tool for identifying CNVs.
  • To optimize CNV detection for clinical applications using targeted sequencing data.

Main Methods:

  • Utilizes changes in read depth to identify CNVs.
  • Focuses on CNVs affecting whole exons.
  • Incorporates interactive visualization of identified CNVs.

Main Results:

  • DECoN effectively identifies CNVs by analyzing read depth alterations.
  • The tool is optimized for clinical settings, facilitating CNV detection.
  • Interactive visualization aids in the interpretation of CNV findings.

Conclusions:

  • DECoN provides a robust method for detecting exon-level CNVs from targeted sequencing.
  • The software's clinical optimization and visualization features enhance its utility in genetic diagnostics.