Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues

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...

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Bibliographic Details
Published in:PloS one 2013-01, Vol.8 (1), p.e52517-e52517
Main Authors: Kolbert, Christopher P, Feddersen, Rod M, Rakhshan, Fariborz, Grill, Diane E, Simon, Gyorgy, Middha, Sumit, Jang, Jin Sung, Simon, Vernadette, Schultz, Debra A, Zschunke, Michael, Lingle, Wilma, Carr, Jennifer M, Thompson, E Aubrey, Oberg, Ann L, Eckloff, Bruce W, Wieben, Eric D, Li, Peter, Yang, Ping, Jen, Jin
Format: Article
Language:English
Subjects:
Biological activity
Biology
Biotechnology
Cell Line
Cell lines
Comparative analysis
Disease
Formaldehyde
Gene expression
Gene Expression Profiling
Genes
Genetic research
Genomes
Genomics
Health sciences
High-Throughput Nucleotide Sequencing
Humans
Informatics
Lung cancer
Measurement
Medical research
MicroRNA
MicroRNAs
MicroRNAs - genetics
miRNA
Oligonucleotide Array Sequence Analysis
Paraffin
Paraffin Embedding
Platforms
Reproducibility
Reproducibility of Results
Ribonucleic acid
RNA
Studies
Tissue Fixation
Tissues
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0052517