Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates

Stephen J. Walker, Yulei Wang, Kathleen A. Grant, Frances Chan, Gary M. Hellmann

    Research output: Contribution to journalArticle

    38 Scopus citations

    Abstract

    The high degree of sequence similarity between human and nonhuman primate (NHP) genomic DNA suggests that human genome sequence-based DNA microarrays may be used effectively to study gene expression in NHP disease models. In the present study, two distinct commercially available human genome microarray platforms, the Affymetrix HG U133A GeneChip® System utilizing Human Genome U133A GeneChips® and the Applied Biosystems Expression Array System utilizing the Human Genome Survey Microarray, were used to identify and characterize gene expression changes in the anterior cerebellum of a macaque monkey model of human alcoholism. The Affymetrix microarray consists of eleven short oligonucleotide probe sets for each gene while the Applied Biosystems Microarray uses a single long oligonucleotide per gene. Cross-mapping of probes revealed a total of 11,542 genes that are represented on both microarray platforms. Absolute measures of gene expression ("present calls") from the cerebellum RNA samples were 65-70% (Applied Biosystems Expression Array System) and 27-30% (AffymetrixGeneChip® System) among these common gene targets. Analysis of variance (ANOVA; p < 0.05; >1.2 fold change; detected on at least 50% of the arrays) indicated 932 and 515 differentially expressed genes for the Applied Biosystems and Affymetrix microarrays, respectively. Significance analysis of microarrays (SAM) identified 255 significant genes at 5% false discovery rate (FDR) for the Applied Biosystems data set and five significant genes at 60% FDR (minimum FDR) for the Affymetrix data set. TaqMan® assay-based real-time PCR validation of a number of differentially-expressed genes yielded results that agreed well with the array data in the majority of comparisons. This study demonstrates that human sequence-based DNA arrays can be used effectively to detect differential gene expression in an NHP disease model and provides evidence that the use of this long oligonucleotide-based microarray platform may be more suitable for cross-species gene expression studies than a short oligonucleotide-based system.

    Original languageEnglish (US)
    Pages (from-to)179-189
    Number of pages11
    JournalJournal of Neuroscience Methods
    Volume152
    Issue number1-2
    DOIs
    StatePublished - Apr 15 2006

    Keywords

    • Alcoholism
    • Cerebellum
    • Gene expression
    • Microarray
    • Nonhuman primate
    • Oligonucleotide

    ASJC Scopus subject areas

    • Neuroscience(all)

    Fingerprint Dive into the research topics of 'Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates'. Together they form a unique fingerprint.

  • Cite this