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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: Jun 14, 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

Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples.

Soroush Nasri1, Ahmad Anjomshoaa, Sarah Song

  • 1Cancer Genetics Laboratory, Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand. nasso300@student.otago.ac.nz

Cancer Genetics and Cytogenetics
|March 23, 2010
PubMed
Summary
This summary is machine-generated.

Agilent oligonucleotide arrays provide reliable genomic profiling from formalin-fixed paraffin-embedded (FFPE) DNA. Affymetrix SNP arrays show increased alterations, making them less suitable for FFPE genomic studies.

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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

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Related Experiment Videos

Last Updated: Jun 14, 2026

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

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Published on: August 5, 2008

Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence In Situ Hybridization
03:55

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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Archival specimens like formalin-fixed paraffin-embedded (FFPE) DNA are valuable for genomic studies.
  • DNA quality from FFPE tissues can be compromised, impacting array-based analyses.
  • No consensus exists on the best platform for FFPE DNA array analysis.

Purpose of the Study:

  • To compare genomic profiles from FFPE and fresh-frozen (FF) tissues.
  • To evaluate the performance of Affymetrix SNP 6.0 and Agilent 4x44K arrays on FFPE DNA.
  • To determine the most suitable platform for FFPE DNA genomic studies.

Main Methods:

  • DNA extraction from matched FFPE-FF pairs of normal intestinal epithelium.
  • Analysis using Affymetrix SNP 6.0 and Agilent 4x44K oligonucleotide arrays.
  • Comparison of genomic profiles between tissue types and platforms.

Main Results:

  • Affymetrix SNP 6.0 platform showed increased copy number alterations in FFPE DNA compared to FF DNA.
  • Agilent 4x44K oligonucleotide arrays yielded highly similar genomic profiles for both FFPE and FF DNA.
  • Both platforms performed comparably on FF material.

Conclusions:

  • Agilent oligonucleotide arrays are reliable for FFPE DNA comparative genomic hybridization.
  • Affymetrix SNP-based arrays appear less suitable for FFPE DNA analysis due to increased apparent alterations.
  • Platform choice is critical for accurate FFPE genomic studies.