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Related Concept Videos

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

Updated: Jul 18, 2026

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation.

Edurne Arriola1, Maryou B K Lambros, Chris Jones

  • 1The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK.

Laboratory Investigation; a Journal of Technical Methods and Pathology
|December 16, 2006
PubMed
Summary

Bacteriophage Phi29 DNA polymerase amplification can introduce copy number biases in genomic analysis. For accurate results in comparative genomic hybridization (aCGH), use amplified reference DNA with similar starting amounts to the test sample.

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Last Updated: Jul 18, 2026

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

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Published on: August 5, 2008

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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
09:27

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Area of Science:

  • Genomics
  • Molecular Biology
  • Biotechnology

Background:

  • High-throughput genomic technologies require sufficient high-quality DNA yields.
  • Microdissected samples often yield insufficient DNA for genome-wide studies.
  • PCR-based amplification methods can lead to nonuniform genomic representation.

Purpose of the Study:

  • To evaluate the genome representation of Phi29 DNA polymerase amplification on a bacterial artificial chromosome microarray comparative genomic hybridization (aCGH) platform.
  • To determine optimal conditions for Phi29 amplification in aCGH analysis.

Main Methods:

  • Phi29 amplification of female genomic DNA at varying concentrations (0.5–50 ng).
  • Comparative genomic hybridization (aCGH) using a 16K BAC platform.
  • Analysis of amplified and unamplified test and reference DNA samples, including microdissected tumor samples.

Main Results:

  • Phi29 amplification of test DNA with unamplified reference DNA introduced copy number biases, especially with lower starting DNA amounts.
  • Biases were significantly reduced when both test and reference DNA were amplified using similar starting concentrations.
  • Accurate genomic profiles for tumor samples were achieved when both test and reference DNA were amplified.

Conclusions:

  • Phi29 amplification can induce copy number biases, making unamplified DNA the gold standard for copy number analysis.
  • For accurate aCGH results with Phi29 amplification, use reference DNA amplified with the same method and similar starting template amounts.