title: MicroRNA expression profiling in archival tissue specimens: methods and data processing.
abstract: The discovery that the human genome codes for thousands (if not millions) of previously unrecognized non-protein coding RNAs with regulatory functions has changed our understanding of many physiological and pathological processes. A prominent class of non-coding RNAs with important functions in cancer initiation and progression comprised by very short single-stranded, mRNA translation modulating RNAs, termed microRNAs. The determination of microRNA expression profiles is now widely used in biology and pathology, employing a range of methodologies. A steadily growing number of studies describe the analysis of formalin-fixed paraffin-embedded, so-called "archival" specimens. However, procedures for data processing and calculations are far from standardized and differ considerably between published studies, making comparisons and meta-analyses still quite difficult. In this review, we provide a short overview of profiling methods used for archival samples and describe in detail a modified method for normalization and processing of raw data obtained by fluorescence-labeled bead technology from Luminex.Inc.
authors.affiliation: Department of Clinical Chemistry/Central Laboratories, Universitätsklinikum Hamburg-Eppendorf, 20246 Hamburg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Streichert
authors.forename: Benjamin
authors.initials: B
authors.lastname: Otto
authors.forename: Ulrich
authors.initials: U
authors.lastname: Lehmann
mesh_terms: D018070:Biological Specimen Banks; D003627:Data Interpretation, Statistical; D057225:Data Mining; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D025341:Principal Component Analysis; D016707:Tissue Fixation / Q000379:methods
chemical_list: D035683:MicroRNAs; D005557:Formaldehyde