Evaluation of DNA microarray results with quantitative gene expression platforms (original) (raw)

• Analysis
• Published: 08 September 2006
• Yuling Luo2 na1,
• James C Willey3 na1,
• Bradley Austermiller3,
• Catalin C Barbacioru1,
• Cecilie Boysen4,
• Kathryn Hunkapiller1,
• Roderick V Jensen5,
• Charles R Knight6,
• Kathleen Y Lee1,
• Yunqing Ma2,
• Botoul Maqsodi2,
• Adam Papallo5,
• Elizabeth Herness Peters6,
• Karen Poulter1,
• Patricia L Ruppel7,
• Raymond R Samaha1,
• Leming Shi8,
• Wen Yang2,
• Lu Zhang1 &
• …
• Federico M Goodsaid9

Nature Biotechnology volume 24, pages 1115–1122 (2006)Cite this article

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Abstract

We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the MicroArray Quality Control (MAQC) data set. The limit of detection, assay range, precision, accuracy and fold-change correlations were assessed for 997 TaqMan Gene Expression Assays, 205 Standardized RT (Sta)RT-PCR assays and 244 QuantiGene assays. TaqMan is a registered trademark of Roche Molecular Systems, Inc. We observed high correlation between quantitative gene expression values and microarray platform results and found few discordant measurements among all platforms. The main cause of variability was differences in probe sequence and thus target location. A second source of variability was the limited and variable sensitivity of the different microarray platforms for detecting weakly expressed genes, which affected interplatform and intersite reproducibility of differentially expressed genes. From this analysis, we conclude that the MAQC microarray data set has been validated by alternative quantitative gene expression platforms thus supporting the use of microarray platforms for the quantitative characterization of gene expression.

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Acknowledgements

We would like to acknowledge the contribution to this manuscript from the following members of the MAQC team: Shawn B. Baker, Anne Bergstrom Lucas, Jim Collins, Eugene Chudin, Stephanie Fulmer-Smentek, Damir Herman, Richard Shippy, Chunlin Xiao and Necip Mehmet.

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Author notes

1. Roger D Canales, Yuling Luo and James C Willey: These authors contributed equally to this work.

Authors and Affiliations

1. Applied Biosystems, 850 Lincoln Centre Dr., Foster City, 94404, California, USA
   Roger D Canales, Catalin C Barbacioru, Kathryn Hunkapiller, Kathleen Y Lee, Karen Poulter, Raymond R Samaha & Lu Zhang
2. Panomics, Inc., 6519 Dumbarton Circle, Fremont, 94555, California, USA
   Yuling Luo, Yunqing Ma, Botoul Maqsodi & Wen Yang
3. University of Toledo, Toledo, 43614, Ohio, USA
   James C Willey & Bradley Austermiller
4. ViaLogy Corp., 2400 Lincoln Avenue, Altadena, 91001, California, USA
   Cecilie Boysen
5. University of Massachusetts-Boston, 100 Morrissey Blvd., Boston, 02125, Massachusetts, USA
   Roderick V Jensen & Adam Papallo
6. Gene Express, Inc., 975 Research Drive, Toledo, 43614, Ohio, USA
   Charles R Knight & Elizabeth Herness Peters
7. Innovative Analytics, 7107 Elm Valley Dr., Kalamazoo, 49009, Michigan, USA
   Patricia L Ruppel
8. National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, 72079, Arkansas, USA
   Leming Shi
9. Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, 20993, Maryland, USA
   Federico M Goodsaid

Authors

1. Roger D Canales
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2. Yuling Luo
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3. James C Willey
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4. Bradley Austermiller
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5. Catalin C Barbacioru
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6. Cecilie Boysen
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7. Kathryn Hunkapiller
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8. Roderick V Jensen
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9. Charles R Knight
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10. Kathleen Y Lee
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11. Yunqing Ma
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12. Botoul Maqsodi
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13. Adam Papallo
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14. Elizabeth Herness Peters
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15. Karen Poulter
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16. Patricia L Ruppel
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17. Raymond R Samaha
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18. Leming Shi
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19. Wen Yang
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20. Lu Zhang
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21. Federico M Goodsaid
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Corresponding author

Correspondence toFederico M Goodsaid.

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Competing interests

J.C.W. is a consultant for and has significant financial interest in Gene Express, Inc.

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Canales, R., Luo, Y., Willey, J. et al. Evaluation of DNA microarray results with quantitative gene expression platforms.Nat Biotechnol 24, 1115–1122 (2006). https://doi.org/10.1038/nbt1236

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• Published: 08 September 2006
• Issue Date: 01 September 2006
• DOI: https://doi.org/10.1038/nbt1236