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Platform influence on DNA microarray data in postmortem brain research.

Deborah Hollingshead1, David A Lewis, Károly Mirnics

  • 1Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA 15261, USA.

Neurobiology of Disease
|March 10, 2005
PubMed
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Different DNA microarray platforms show high reproducibility but fail to consistently identify the same differentially expressed genes in human postmortem brain tissue. This highlights the need for careful consideration when comparing transcriptome data across studies.

Area of Science:

  • Genomics
  • Neuroscience
  • Bioinformatics

Background:

  • Human biological diversity impacts transcriptome data.
  • Small expression changes are difficult to measure reliably in postmortem brain.
  • Microarray platform design and analysis tools influence experimental outcomes.

Purpose of the Study:

  • To evaluate the sensitivity, dynamic range, and reproducibility of three common DNA microarray platforms.
  • To compare gene expression profiles from human postmortem brain samples across different platforms.

Main Methods:

  • Comparison of two human postmortem brain samples.
  • Utilized dual-fluorescence cDNA microarrays, Affymetrix GeneChips, and CodeLink oligonucleotide arrays.
  • Analyzed data for sensitivity, dynamic range, and reproducibility.

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Main Results:

  • All three platforms demonstrated good dynamic range and high correlation in replicate experiments.
  • Platforms failed to consistently identify the same differentially expressed genes between samples.
  • Despite reproducibility, platforms appear to measure different aspects of gene expression.

Conclusions:

  • Microarray platform design and function lead to distinct measurements.
  • Researchers must account for platform-specific differences when comparing transcriptome data.
  • This variability impacts the ability to obtain convergent transcriptome data from postmortem brain studies.