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DNA Microarrays

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 4, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Microarray profiling of DNA extracted from FFPE tissues using SNP 6.0 Affymetrix platform.

Marianne Tuefferd¹, An de Bondt, Ilse Van den Wyngaert

¹Johnson & Johnson Pharmaceutical Research & Development, Beerse, Belgium. mtueffe1@its.jnj.com

Methods in Molecular Biology (Clifton, N.J.)

|March 4, 2011

Summary

Optimizing protocols for Affymetrix SNP 6.0 arrays enables genome-wide association studies (GWAS) and tumor analysis. This technology can now effectively analyze partially degraded DNA from formalin-fixed paraffin-embedded (FFPE) samples.

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Area of Science:

Genomics
Molecular Biology
Cancer Research

Background:

High-density oligonucleotide microarrays are crucial for Genome-Wide Association Studies (GWAS) and identifying tumor genome alterations.
The Affymetrix Genome-Wide SNP 6.0 microarray offers high genome coverage and requires minimal DNA input.
Standardized and reproducible hybridization protocols are essential due to DNA digestion and PCR amplification steps, which are sensitive to sample degradation.

Purpose of the Study:

To optimize target preparation and in silico data analysis protocols for the Affymetrix SNP 6.0 microarray.
To enable the effective use of SNP array technology with partially degraded DNA, particularly from formalin-fixed paraffin-embedded (FFPE) samples.
To unlock the potential of analyzing large retrospective sample series using SNP array technology.

Main Methods:

Adjusting the target preparation protocol to enhance hybridization performance.
Modifying the in silico data analysis procedure to maximize biological information extraction.
Utilizing the Affymetrix SNP 6.0 microarray technology.

Main Results:

Optimized protocols allow for successful genome variation analysis using the Affymetrix SNP 6.0 microarray.
Partially degraded DNA, common in FFPE tissues, can be effectively analyzed.
Improved hybridization and data analysis yield more biological information from SNP array signals.

Conclusions:

The Affymetrix SNP 6.0 microarray technology can be successfully applied to FFPE samples with partially degraded DNA.
Optimized protocols significantly improve the feasibility of using SNP arrays for genomic studies on challenging sample types.
This advancement holds significant potential for large-scale retrospective studies in cancer research and other fields.