Evaluation of gene expression data generated from expired Affymetrix GeneChip microarrays using MAQC reference RNA samples

Article (PDF Available)inBMC Bioinformatics 11 Suppl 6(Suppl 6):S10 · October 2010with18 Reads
DOI: 10.1186/1471-2105-11-S6-S10 · Source: PubMed
The 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. Microarray 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. Our 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.

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Available from: Zhining Wen, Dec 19, 2013
    • "This normalisation level was chosen because of a low microarray intensity level, due to the use of expired microarrays. It has, however, been shown that microarray data generated by microarrays more than 4 years past the manufacturer's expiration date had lower signal intensities but were highly specific and consistent with those from unexpired microarrays [33]. We used microarrays within 2 years of the expiry date. "
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    • "The opportunity to study tissue-specific expression in such a comparison was taken by Luo et al. [79] but the annotations were assumed to be correct and a quality control method to verify this was not devised. While quality control methods were previously suggested, they only focussed on the genome (potentially missing alternatively spliced variants that would have been detected by studying the transcriptome) [80,81], or on the proteome (potentially missing mRNAs whose translation is downregulated by microRNAs [83,84] or covered aspects of the data such as GC content [40], noise [12,13] source material quality [62,63,67,70,86], different experimental methods6465667172737476777879 or read quality878889909192939495 , with few investigations focusing on the tissuespecificity issues [75,96], even when two or more methods were used in the same study979899100101. A common shortcoming of many previous attempts is that tissue specificity of the genes was reported102103104105106107108109110111112, or avoided113114115. "
    Article · Jan 2015
    • "In addition, Wen et al. [19] have demonstrated that even for arrays that were expired by several years (and of different lot numbers) the percentage of overlap between lists of differentially expressed genes from the expired and unexpired microarrays was 96.99%. In addition , microarray data generated using the expired microarrays were highly concordant with microarray and TaqMan ® data generated by the MAQC project several years before [19]. "
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