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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%...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
PCR01:32

PCR

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Related Experiment Video

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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
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Amplification ratio control system for copy number variation genotyping.

Philip A I Guthrie1, Tom R Gaunt, Mohammed R Abdollahi

  • 1Bristol Genetic Epidemiology Laboratory and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield Grove, Clifton BS8 2BN, UK. philip.guthrie@bristol.ac.uk

Nucleic Acids Research
|February 9, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a novel universal primer (UP) system for gene copy number variation (CNV) analysis. The amplification ratio control system (ARCS) enables accurate ratiometric quantification without real-time PCR, offering a simple and economical method.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • Accurate determination of gene copy number variation (CNV) is crucial for genetic research and diagnostics.
  • Existing methods like real-time PCR can be complex and costly.
  • A simplified, cost-effective approach for CNV analysis is needed.

Purpose of the Study:

  • To present a generic design for ratiometric analysis to determine gene CNV class.
  • To introduce the amplification ratio control system (ARCS) for precise amplicon quantification.
  • To demonstrate the utility of ARCS for CNV assays.

Main Methods:

  • Utilizing a universal primer (UP) for priming both test and reference amplicons in a duplex PCR.
  • Employing a hairpin structure formed by the UP and its reverse complement (UP') after denaturation.
  • Leveraging differential %(G+C) content for liquid phase thermal melt discrimination.

Main Results:

  • The ARCS enables ratiometric representation of amplicons relative to the template at the PCR plateau phase.
  • This method circumvents the need for real-time PCR for accurate quantitation.
  • Successful CNV assays were demonstrated for haptoglobin duplicon and a chemokine gene.

Conclusions:

  • The ARCS provides a generic, simple, and economical design for ratiometric analysis of gene CNV.
  • The system allows for accurate quantitation without real-time PCR, making it broadly applicable.
  • This approach offers a valuable tool for genetic variation studies.