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Evaluation of gene expression measurements from commercial microarray platforms
Paul K Tan1, Thomas J Downey, Edward L Spitznagel
1Microarray Core Laboratory, National Institute of Diabetes and Digestive and Kidney Disorders, National Institutes of Health, USA.
Nucleic Acids Research
|September 23, 2003
Summary
Commercial microarray platforms show significant differences in gene expression measurements. This study highlights the need for industry standards and independent validation for reliable genomic data.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Numerous commercial microarray platforms exist for genome-wide gene expression analysis.
- These platforms include oligonucleotide and cDNA, single- and two-channel formats.
Purpose of the Study:
- To compare gene expression measurements from three different commercial microarray platforms using identical RNA samples.
- To assess the consistency and reliability of gene expression data across platforms.
Main Methods:
- RNA was extracted from PANC-1 cells under two conditions (serum-rich and serum-deprived).
- Identical RNA preparations were hybridized to microarrays from three major suppliers following manufacturer protocols.
- Gene expression levels for a common subset of 2009 genes were analyzed using each platform's standard software.
Main Results:
- Gene expression measurements showed considerable divergence across the three platforms.
- Correlations in gene expression levels and significant gene expression changes varied between platforms.
- The study identified inconsistencies in data generated by different commercial microarray technologies.
Conclusions:
- There is a need for establishing industrial manufacturing standards for microarray technologies.
- Independent and thorough validation of microarray platforms is crucial for accurate gene expression analysis.
- Differences across platforms necessitate careful consideration when interpreting genome-wide gene expression data.