title: Performance comparison of digital microRNA profiling technologies applied on human breast cancer cell lines.
abstract: MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.
authors.affiliation: Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
authors.forename: Erik
authors.initials: E
authors.lastname: Knutsen
authors.forename: Tonje
authors.initials: T
authors.lastname: Fiskaa
authors.forename: Anita
authors.initials: A
authors.lastname: Ursvik
authors.forename: Tor Erik
authors.initials: TE
authors.lastname: Jørgensen
authors.forename: Maria
authors.initials: M
authors.lastname: Perander
authors.forename: Eiliv
authors.initials: E
authors.lastname: Lund
authors.forename: Ole Morten
authors.initials: OM
authors.lastname: Seternes
authors.forename: Steinar D
authors.initials: SD
authors.lastname: Johansen
authors.forename: Morten
authors.initials: M
authors.lastname: Andreassen
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs