Abstract
BackgroundThe Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. In addition, it was not clear whether the two human reference RNA samples established by the MAQC project in 2005 still maintained their transcriptome integrity over a period of four years. Experiments were conducted to answer these questions.ResultsMicroarray data were generated in 2009 in three replicates for each of the two MAQC samples with either expired Affymetrix U133A or unexpired U133Plus2 microarrays. These results were compared with data obtained in 2005 on the U133Plus2 microarray. The percentage of overlap between the lists of differentially expressed genes (DEGs) from U133Plus2 microarray data generated in 2009 and in 2005 was 97.44%. While there was some degree of fold change compression in the expired U133A microarrays, the percentage of overlap between the lists of DEGs from the expired and unexpired microarrays was as high as 96.99%. Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005.ConclusionsOur results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80°C, were stable over a time frame of at least four years.
Highlights
The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive
Two sources of data were used in this study: gene expression data newly generated in 2009 for this study and data generated by the MicroArray Quality Control (MAQC) project in 2005
Gene expression data generated with unexpired U133Plus2 microarrays (AFX), other microarray platforms, and TaqMan® assays by the MAQC project in 2005 were used as references to assess the stability of the MAQC samples stored at -80°C for four years by comparing new microarray data with those obtained four years ago
Summary
The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of prepurchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis It was not clear whether the two human reference RNA samples established by the MAQC project in 2005 still maintained their transcriptome integrity over a period of four years. Several studies showed poor overlaps of DEGs across different platforms or different laboratories using the same sets of RNA samples [4,5,6,7,8], raising concerns on the reliability of microarray technology [9,10,11,12,13] and leading to the launch of the MicroArray Quality Control (MAQC) project [14,15]. Excellent interlaboratory and inter-platform reproducibility in terms of DEG lists was observed in the MAQC project [15,16]
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