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

ABSTRACT: 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. 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. The new gene expression data were generated with 12 microarrays (2 types of microarrays × 2 samples × 3 replicates). Three replicates for each of the two MAQC samples (A = Stratagene’s Universal Human Reference RNA; B = Ambion’s Human Brain Reference RNA) were profiled in 2009 by using both the expired U133A microarrays (expired in 2004) and the unexpired U133Plus2 microarrays. In addition, 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. The MAQC reference data also allowed for further evaluation of the usefulness of the data generated with expired U133A microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Leming Shi

PROVIDER: E-GEOD-23906 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Wen Zhining Z Wang Charles C Shi Quan Q Huang Ying Y Su Zhenqiang Z Hong Huixiao H Tong Weida W Shi Leming L

BMC bioinformatics 20101007

<h4>Background</h4>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 micro ...[more]

PMID: 20946593

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Project description:The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and analysis issues. We demonstrate the consistency of results within a platform across test sites as well as the high level of cross-platform concordance in terms of genes identified as differentially expressed. The MAQC study provides a rich resource that will help build consensus on the use of microarrays in research, clinical and regulatory settings. Manuscripts related to the MAQC project have been published in Nature Biotechnology, 24(9), September, 2006. More information about the MAQC project can be found at http://edkb.fda.gov/MAQC/.<br><br>Expression data from two distinct reference RNA samples (A and B) in four titration pools were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Sample A = Stratagene Universal Human Reference RNA (UHRR, Catalog #740000), Sample B = Ambion Human Brain Reference RNA (HBRR, Catalog #6050), Sample C = Samples A and B mixed at 75%:25% ratio (A:B); and Sample D = Samples A and B mixed at 25%:75% ratio (A:B). In general, each microarray platform was tested at three sites and each sample was tested in five replicates at each test site. Samples (hybridizations) were named according to the following convention: Platform_Testsite_SampleRelicate. For example, AFX_2_B1 represents the hybridization (array) from platform AFX processed by test site 2 for the first replicate of sample B. Assignment of platform code: ABI = Applied Biosystems (microarray); AFX = Affymetrix; AG1 = Agilent one-color; AGL = Agilent two-color; GEH = GE Healthcare; ILM = Illumina; NCI = NCI two-color (Operon oligos); EPP = Eppendorf; TAQ = TaqMan (Applied Biosystems); QGN = QuantiGene (Panomics); GEX = StaRT-PCR (Gene Express); H25K = TeleChem two-color; H25K1 = TeleChem one-color; BIO = CapitalBio two-color (Operon oligos); BIO1 = CapitalBio one-color (Operon oligos); OPN = Operon two-color (Operon oligos); NMC = Norwegian Microarray Consortium two-color (Operon oligos).

Dataset Information

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

Publications

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

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