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

BMC Bioinformatics

Proceedings

Quan Shi¹  Ying Huang¹  Leming Shi²  Weida Tong²  Zhining Wen²  Huixiao Hong²  Charles Wang³  Zhenqiang Su⁴ 

[1] College of Pharmacy, Western University of Health Sciences, 309 E. Second Street, 91766, Pomona, CA, USA;Division of Systems Biology, National Center for Toxicological Research (NCTR), US Food and Drug Administration (FDA), 3900 NCTR Road, 72079, Jefferson, AR, USA;Functional Genomics Core, Beckman Research Institute, City of Hope Comprehensive Cancer Center, 1710 Flower Avenue, 91010, Duarte, CA, USA;David Geffen School of Medicine at UCLA, 90095, Los Angeles, CA, USA;Z-Tech/ICF International at NCTR/FDA, 3900 NCTR Road, 72079, Jefferson, AR, USA;

关键词: Gene Expression Data;    Microarray Platform;    Affymetrix GeneChip;    Log2 Fold Change;    Log2 Intensity;   

DOI  :  10.1186/1471-2105-11-S6-S10

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Shi et al; licensee BioMed Central Ltd. 2010