title: Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array.
abstract: BACKGROUND
  A number of gene-profiling methodologies have been applied to microRNA research. The diversity of the platforms and analytical methods makes the comparison and integration of cross-platform microRNA profiling data challenging. In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA).
  
  
  RESULTS
  The microRNA profiles of 40 human osteosarcoma xenograft samples were generated by LNA array, beads array, and TLDA. Results show that each of the three platforms perform similarly regarding intra-platform reproducibility or reproducibility of data within one platform while LNA array and TLDA had the best inter-platform reproducibility or reproducibility of data across platforms. The endogenous controls/probes contained in each platform have been observed for their stability under different treatments/environments; those included in TLDA have the best performance with minimal coefficients of variation. Importantly, we identify that the proper selection of normalization methods is critical for improving the inter-platform reproducibility, which is evidenced by the application of two non-linear normalization methods (loess and quantile) that substantially elevated the sensitivity and specificity of the statistical data assessment.
  
  
  CONCLUSIONS
  Each platform is relatively stable in terms of its own microRNA profiling intra-reproducibility; however, the inter-platform reproducibility among different platforms is low. More microRNA specific normalization methods are in demand for cross-platform microRNA microarray data integration and comparison, which will improve the reproducibility and consistency between platforms.
authors.affiliation: Department of Mathematics and Statistics, University of South Alabama College of Arts and Sciences, Mobile, Alabama, United States of America.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Paul
authors.initials: P
authors.lastname: Howel
authors.forename: Skjalg
authors.initials: S
authors.lastname: Bruheim
authors.forename: Jingfang
authors.initials: J
authors.lastname: Ju
authors.forename: Laurie B
authors.initials: LB
authors.lastname: Owen
authors.forename: Oystein
authors.initials: O
authors.lastname: Fodstad
authors.forename: Yaguang
authors.initials: Y
authors.lastname: Xi
mesh_terms: D002471:Cell Transformation, Neoplastic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008863:Microspheres; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D012516:Osteosarcoma / Q000235:genetics / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D035683:MicroRNAs; D009841:Oligonucleotides; C477371:locked nucleic acid