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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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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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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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Related Experiment Video

Updated: Mar 15, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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Copy Number Studies in Noisy Samples.

Philip Ginsbach1, Bowang Chen2, Yanxiang Jiang3

  • 1Neurology Department, University of Heidelberg, INF 400, Heidelberg D69120, Germany. Philip.Ginsbach@t-online.de.

Microarrays (Basel, Switzerland)
|September 9, 2016
PubMed
Summary

A new software, "noise-free-cnv," effectively reduces system noise in Affymetrix 6.0 data for copy number variation (CNV) detection. This noise reduction improves data quality and aids in accurate CNV analysis.

Keywords:
copy number variation (CNV)noise reductionnoise-free-cnv softwareper-SNP noisevalidation of CNV findingsvariancewave noise

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • System noise in Affymetrix 6.0 data impacts copy number variation (CNV) detection accuracy.
  • Previous studies have faced challenges in classifying sample quality for reliable CNV analysis.

Purpose of the Study:

  • To develop and evaluate novel software for visualizing and reducing system noise in Affymetrix 6.0 data.
  • To improve the accuracy and reliability of copy number variation (CNV) detection.

Main Methods:

  • Analysis of system noise in 77 Affymetrix 6.0 samples.
  • Development of "noise-free-cnv" software for noise visualization and reduction.
  • Assessment of sample eligibility based on DNA preparation, SNP genotyping, and signal intensity variance.

Main Results:

  • "noise-free-cnv" software successfully visualized and reduced system noise, including wave and per-SNP noise patterns.
  • Eligible samples, often from fresh DNA, showed higher SNP genotyping rates and lower signal intensity variance.
  • Noise reduction and visual inspection are recommended prior to molecular validation of CNV calls.

Conclusions:

  • The "noise-free-cnv" software is a valuable tool for mitigating system noise in CNV studies.
  • A two-step validation process involving noise reduction and visual inspection enhances CNV detection reliability.
  • Optimizing sample quality and employing advanced noise reduction techniques are crucial for accurate genomic analysis.