title: Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis.
abstract: BACKGROUND
  MicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease processes. A technical challenge remains for high-throughput miRNA expression analysis as the number of miRNAs continues to increase with in silico prediction and experimental verification. Our study critically evaluated the performance of a novel miRNA expression profiling approach, quantitative RT-PCR array (qPCR-array), compared to miRNA detection with oligonucleotide microchip (microarray).
  
  
  RESULTS
  High reproducibility with qPCR-array was demonstrated by comparing replicate results from the same RNA sample. Pre-amplification of the miRNA cDNA improved sensitivity of the qPCR-array and increased the number of detectable miRNAs. Furthermore, the relative expression levels of miRNAs were maintained after pre-amplification. When the performance of qPCR-array and microarrays were compared using different aliquots of the same RNA, a low correlation between the two methods (r=-0.443) indicated considerable variability between the two assay platforms. Higher variation between replicates was observed in miRNAs with low expression in both assays. Finally, a higher false positive rate of differential miRNA expression was observed using the microarray compared to the qPCR-array.
  
  
  CONCLUSIONS
  Our studies demonstrated high reproducibility of TaqMan qPCR-array. Comparison between different reverse transcription reactions and qPCR-arrays performed on different days indicated that reverse transcription reactions did not introduce significant variation in the results. The use of cDNA pre-amplification increased the sensitivity of miRNA detection. Although there was variability associated with pre-amplification in low abundance miRNAs, the latter did not involve any systemic bias in the estimation of miRNA expression. Comparison between microarray and qPCR-array indicated superior sensitivity and specificity of qPCR-array.
authors.affiliation: Department of Surgery, University of Texas Health Science Center, San Antonio, TX 78229, USA. cheny4@uthscsa.edu
authors.forename: Yongxin
authors.initials: Y
authors.lastname: Chen
authors.forename: Jonathan A L
authors.initials: JA
authors.lastname: Gelfond
authors.forename: Linda M
authors.initials: LM
authors.lastname: McManus
authors.forename: Paula K
authors.initials: PK
authors.lastname: Shireman
mesh_terms: D000818:Animals; D002460:Cell Line; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs