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Originally published online as doi:10.2353/jmoldx.2008.080077 on October 2, 2008

Published online before print October 2, 2008
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Journal of Molecular Diagnostics 2008, Vol. 10, No. 6
Copyright © 2008 American Society for Investigative Pathology & Association for Molecular Pathology
DOI: 10.2353/jmoldx.2008.080077

An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples

Xiao Zhang*, Jiamin Chen*, Tom Radcliffe*§, Dave P. LeBrun*{dagger}{ddagger}, Victor A. Tron*{dagger}{ddagger} and Harriet Feilotter*{dagger}{ddagger}

From the Department of Pathology and Molecular Medicine, * Queen’s Laboratory for Molecular Pathology, {dagger} Queen’s Cancer Research Institute, {ddagger} Queen’s University and Kingston General Hospital; and Predictive Patterns Software, Inc, § Kingston, Ontario, Canada

MicroRNAs (miRNAs) are small, noncoding RNAs that suppress gene expression at the posttranscriptional level via an antisense RNA-RNA interaction. miRNAs used for array-based profiling are generally purified from either snap-frozen or fresh samples. Because tissues found in most pathology departments are available only in formalin-fixed and paraffin-embedded (FFPE) states, we sought to evaluate miRNA derived from FFPE samples for microarray analysis. In this study, miRNAs extracted from matched snap-frozen and FFPE samples were profiled using the Agilent miRNA array platform (Agilent, Santa Clara, CA). Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. Seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling, and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results; technical replicates showed high correlations with one another (Kendall tau, 0.722 to 0.853; Spearman rank correlation coefficient, 0.891 to 0.954). Our results showed consistent high correlations between matched frozen and FFPE samples (Kendall tau, 0.669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling.






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Copyright © 2008 by the American Society for Investigative Pathology and the Association for Molecular Pathology.