Platform influence on DNA microarray data in postmortem brain research

Deborah Hollingshead, David A. Lewis, Károly Mirnics

Research output: Contribution to journalArticle

46 Scopus citations

Abstract

In addition to the substantial biological diversity among humans, our limited ability to reliably measure expression changes of small magnitude significantly reduces our capacity to obtain convergent sets of transcriptome data in postmortem brain. In particular, differences in the structure and sensitivity/reproducibility of microarray platforms, and in the variety of tools used to analyze microarray data, strongly influence experimental outcome. In order to better understand the sensitivity, dynamic range, and reproducibility of three common DNA microarray platforms, we compared two human postmortem samples on cDNA microarrays with dual-fluorescence, oligonucleotide GeneChips® (Affymetrix), and single-color gel matrix deposited CodeLink® oligonucleotide arrays. All three microarray platforms reported a good dynamic range and high correlation in replicate experiments, but they failed to consistently identify the same genes as differentially expressed between the same samples. Given their reproducibility and proven accuracy, different microarray platforms appear to be measuring different things by nature of their design and function. This needs to be taken into account when comparing data across studies.

Original languageEnglish (US)
Pages (from-to)649-655
Number of pages7
JournalNeurobiology of Disease
Volume18
Issue number3
DOIs
Publication statusPublished - Apr 2005

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Keywords

  • CodeLink
  • DNA microarray
  • Expression profiling
  • GeneChip
  • Hybridization
  • Platform comparison
  • Postmortem
  • Schizophrenia
  • cDNA array

ASJC Scopus subject areas

  • Neurology

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