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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%...
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...

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Related Experiment Video

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Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Enhancer chip: detecting human copy number variations in regulatory elements.

Marco Savarese1, Giulio Piluso, Daniela Orteschi

  • 1Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy.

Plos One
|January 4, 2013
PubMed
Summary
This summary is machine-generated.

Copy number variations (CNVs) in gene enhancer regions may cause disease. We developed Enhancer Chip, a novel array-based comparative genomic hybridization (aCGH) test, to detect these disease-associated CNVs.

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Area of Science:

  • Genomics
  • Human Genetics
  • Molecular Biology

Background:

  • Non-coding DNA sequences, particularly gene enhancers, play critical roles in cellular function.
  • Variations in enhancer sequences, including copy-number variations (CNVs), are increasingly linked to various human diseases.
  • Understanding the distribution and impact of CNVs on enhancers is crucial for disease research.

Purpose of the Study:

  • To analyze the genomic distribution of enhancer loci and compare it with known CNVs.
  • To develop a cost-effective method for identifying CNVs that overlap with enhancer elements.
  • To investigate the potential pathogenic role of copy number variable enhancers.

Main Methods:

  • Comparative analysis of enhancer loci distribution and previously identified CNVs.
  • Development and validation of a customized oligonucleotide Array-Based Comparative Genomic Hybridization (aCGH) array, named Enhancer Chip.
  • Enhancer Chip offers 300 Kb genome-wide resolution and tenfold higher resolution for specific disease regions, interrogating over 1,250 enhancers.

Main Results:

  • Analysis suggests negative selection of copy number variable enhancers.
  • Enhancer Chip efficiently detects duplications and deletions encompassing enhancer loci.
  • The developed aCGH is a powerful tool for detecting and characterizing copy number variable enhancers.

Conclusions:

  • CNVs affecting enhancer elements are implicated in various disorders.
  • Enhancer Chip provides a high-resolution, cost-effective method for analyzing CNVs in enhancer regions.
  • This tool facilitates the investigation of the pathogenic potential of copy number variable enhancers.