title: Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.
abstract: Next-generation sequencing is increasingly employed in biomedical investigations. Strong concordance between microarray and mRNA-seq levels has been reported in high quality specimens but information is lacking on formalin-fixed, paraffin-embedded (FFPE) tissues, and particularly for microRNA (miRNA) analysis. We conducted a preliminary examination of the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays. Quantitative agreement between platforms is moderate (Spearman correlation 0.514-0.596) and there is discordance of detection calls on a subset of miRNAs. Quantitative PCR (q-RT-PCR) performed for several discordant miRNAs confirmed the presence of most sequences detected by miRNA-seq but not by DASL but also that miRNA-seq did not detect some sequences, which DASL confidently detected. Our results suggest that miRNA-seq is specific, with few false positive calls, but it may not detect certain abundant miRNAs in FFPE tissue. Further work is necessary to fully address these issues that are pertinent for translational research.
authors.affiliation: Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA. andrew.kelly2010@gmail.com
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Kelly
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Hill
authors.forename: Mick
authors.initials: M
authors.lastname: Correll
authors.forename: Lan
authors.initials: L
authors.lastname: Hu
authors.forename: Yaoyu E
authors.initials: YE
authors.lastname: Wang
authors.forename: Renee
authors.initials: R
authors.lastname: Rubio
authors.forename: Shenghua
authors.initials: S
authors.lastname: Duan
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Spentzos
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D015925:Cryopreservation; D018076:DNA, Complementary / Q000235:genetics*; D005260:Female; D005557:Formaldehyde / Q000737:chemistry; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D046228:Microarray Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D012333:RNA, Messenger / Q000235:genetics*; D016707:Tissue Fixation
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs; D012333:RNA, Messenger; D005557:Formaldehyde
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