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Evaluation of quality-control criteria for microarray gene expression analysis.

Catherine I Dumur1, Suhail Nasim, Al M Best

  • 1Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA.

Clinical Chemistry
|September 15, 2004
PubMed
Summary
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Establishing quality-control criteria for RNA ensures reproducible microarray results for clinical applications. Adhering to these standards, like rRNA percentage and median cDNA/cRNA size, enhances data reliability.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Reproducibility of microarray results is crucial for clinical applications but quality-control criteria are underdeveloped.
  • Current methods lack standardized quality-control measures for ensuring reliable microarray data.

Purpose of the Study:

  • To develop and evaluate quality-control criteria for microarray data analysis.
  • To assess the impact of these criteria on the reproducibility of results.
  • To identify sources of variation in microarray experiments.

Main Methods:

  • Developed quality-control criteria including A260/A280 ratios, rRNA percentage, and median cDNA/cRNA size.
  • Evaluated criteria using RNA from cell lines, tumors, and reference RNA.
  • Performed precision studies on Affymetrix HG-U133A microarrays with reference RNA across different conditions.

Related Experiment Videos

  • Utilized ANOVA to identify main sources of variation.

    • Main Results:

    • Good-quality samples exhibited >30% rRNA and specific median cDNA/cRNA sizes (2.0 and 3.0 kb).
    • Day-to-day variability was the primary source of variation, with minimal impact on control genes.
    • The Affymetrix Genechip system demonstrated high reproducibility with RNA meeting defined quality-control criteria (P >0.01).

    Conclusions:

    • Defined quality-control criteria are essential for sample quality assessment.
    • These criteria help differentiate between analytical and biological variability in microarray data.
    • Implementation of these criteria is necessary for reliable clinical application of microarrays.