Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues

Christopher P. Kolbert, Rod M. Feddersen, Fariborz Rakhshan, Diane E. Grill, Gyorgy Simon, Sumit Middha, Jin Sung Jang, Vernadette Simon, Debra A. Schultz, Michael Zschunke, Wilma Lingle, Jennifer M. Carr, E. Aubrey Thompson, Ann L. Oberg, Bruce W. Eckloff, Eric D. Wieben, Peter Li, Ping Yang, Jin Jen

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Abstract

MicroRNAs play a role in regulating diverse biological processes and have considerable utility as molecular markers for diagnosis and monitoring of human disease. Several technologies are available commercially for measuring microRNA expression. However, cross-platform comparisons do not necessarily correlate well, making it difficult to determine which platform most closely represents the true microRNA expression level in a tissue. To address this issue, we have analyzed RNA derived from cell lines, as well as fresh frozen and formalin-fixed paraffin embedded tissues, using Affymetrix, Agilent, and Illumina microRNA arrays, NanoString counting, and Illumina Next Generation Sequencing. We compared the performance within- and between the different platforms, and then verified these results with those of quantitative PCR data. Our results demonstrate that the within-platform reproducibility for each method is consistently high and although the gene expression profiles from each platform show unique traits, comparison of genes that were commonly detectable showed that detection of microRNA transcripts was similar across multiple platforms.

Original languageEnglish (US)
Article numbere52517
JournalPloS one
Volume8
Issue number1
DOIs
StatePublished - Jan 31 2013

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Kolbert, C. P., Feddersen, R. M., Rakhshan, F., Grill, D. E., Simon, G., Middha, S., Jang, J. S., Simon, V., Schultz, D. A., Zschunke, M., Lingle, W., Carr, J. M., Thompson, E. A., Oberg, A. L., Eckloff, B. W., Wieben, E. D., Li, P., Yang, P., & Jen, J. (2013). Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues. PloS one, 8(1), [e52517]. https://doi.org/10.1371/journal.pone.0052517