Ribonucleic Acid Microarray Analysis From Lymph Node Samples Obtained by Endobronchial Ultrasonography-Guided Transbronchial Needle Aspiration

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Abstract

Purpose.

The aim of this study was to evaluate the feasibility of messenger RNA (mRNA) and microRNA (miRNA) expression analysis by microarray using samples obtained by endobronchial ultrasonography-guided transbronchial needle aspiration (EBUS-TBNA).

Description.

We isolated total RNA from 24 archived clinical EBUS-TBNA samples. The purified RNA that met the quality threshold was used for two different kinds of microarray analyses: whole transcript–based (WT) array for mRNA expression and miRNA expression array.

Evaluation.

The RNA from 17 of the 24 samples (71%; 12 adenocarcinoma, 3 squamous cell carcinoma, 2 poorly differentiated carcinoma) met the quality threshold. After performing a one-way analysis of variance, we found genes with significant differences in histologic subtype (p< 0.01) for each of the WT and miRNA expression data sets. The samples clustered discretely according to their histologic subtypes by hierarchical clustering. After adjusting for multiple testing using the Benjamini-Hochberg false discovery rate correction, there remained 16 WT genes and 4 miRNAs with a false discovery rate of 5% or less.

Conclusions.

Samples of EBUS-TBNA can be used for comprehensive WT and miRNA expression analysis using microarray technology.

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