title: A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients.
abstract: Although formalin fixed paraffin embedded (FFPE) tissue is a major biological source in cancer research, it is challenging to work with due to macromolecular fragmentation and nucleic acid crosslinking. Therefore, it is important to characterise the quality of data that can be obtained from FFPE samples. We have compared three independent platforms (next generation sequencing, microarray and NanoString) for profiling microRNAs (miRNAs) using clinical FFPE samples from hepatoblastoma (HB) patients. The number of detected miRNAs ranged from 228 to 345 (median = 294) using the next generation sequencing platform, whereas 79 to 125 (median = 112) miRNAs were identified using microarrays in three HB samples, including technical replicates. NanoString identified 299 to 372 miRNAs in two samples. Between the platforms, we observed high reproducibility and significant levels of shared detection. However, for commonly detected miRNAs, a strong correlation between platforms was not observed. Analysis of 10 additional HB samples with NanoString identified significantly overlapping miRNA expression profiles, and an alternative pattern was identified in a poorly differentiated HB with an aggressive phenotype. This investigation serves as a roadmap for future studies investigating miRNA expression in clinical FFPE samples, and as a guideline for the selection of an appropriate platform.
authors.affiliation: 1] Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand [2] Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
authors.forename: Aniruddha
authors.initials: A
authors.lastname: Chatterjee
authors.affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.
authors.forename: Anna L
authors.initials: AL
authors.lastname: Leichter
authors.affiliation: Bioinformatics Institute, University of Auckland, New Zealand.
authors.forename: Vicky
authors.initials: V
authors.lastname: Fan
authors.affiliation: Bioinformatics Institute, University of Auckland, New Zealand.
authors.forename: Peter
authors.initials: P
authors.lastname: Tsai
authors.affiliation: Children's Cancer Research Group, University of Otago, Christchurch, New Zealand.
authors.forename: Rachel V
authors.initials: RV
authors.lastname: Purcell
authors.affiliation: Royal Children's Hospital, Melbourne, Victoria, Australia.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sullivan
authors.affiliation: 1] Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand [2] Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Eccles
mesh_terms: D005260:Female; D020869:Gene Expression Profiling; D018197:Hepatoblastoma / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008113:Liver Neoplasms / Q000235:genetics*; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D035683:MicroRNAs