Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens. Homo sapiens

MicroRNAs are useful biomarkers for various disease states, and their preservation in formalin-fixed, paraffin-embedded (FFPE) tissue makes them particularly useful for clinicogenetic studies. Although global microRNA expression in FFPE samples is routinely measured with microarrays, the utility of RNA sequencing for such profiling has yet to be established. In this study, to appraise the suitability of RNA sequencing, microRNAs in RNA from pathologic stage I lung adenocarcinoma FFPE samples were quantified with 8x60K Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray and Illumina® HiSeq™ 2000 sequencing platforms. Overall design: Total RNA was extracted from eight tumor specimens and all eight were used in duplicate for microRNA quantification with the Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray platform. Microarray experiments were conducted twice, once for each set of duplicates. All eight RNA samples, with two in duplicate, were also used for RNA sequencing on the Illumina® HiSeq™ 2000 sequencing platform.