A cross comparison of technologies for the detection of microRNAs in FFPE samples from hepatoblastoma patients

Abstract

MicroRNAs (miRNAs) are small non-coding RNA that regulate gene expression. Profiling miRNA patterns has provided insight into cancer. Formalin fixed paraffin embedded (FFPE) tissue is a major source of biological material, including miRNAs, in cancer research. However, analysing FFPE material can be challenging for researchers due to sample degradation and nucleic acid crosslinking. It is therefore valuable to characterise and document the quality of data that can be obtained from FPPE samples. In this study we compared the detection level of microRNAs between three independent platforms, next generation sequencing, microarray and NanoString, using FFPE samples from hepatoblastoma patients. Between 228 and 345 miRNAs were identified using the next generation sequencing platform, 79 to 125 miRNAs were identified with microarray and NanoString identified the most (135 to 411) miRNAs. Technical reproducibility was very high between the platforms. There were significant shared detection levels between the platforms, and a weak positive correlation was observed in the relative abundance level of commonly detected miRNAs between the platforms. This work highlights the advantages and disadvantages of the three miRNA detection platforms through performance comparisons. This will inform and aid the design of future studies aiming to quantify miRNA expression, and can be used as a guideline for selection of an appropriate platform.