Comparative microRNA Profiling by TaqMan Low Density Arrays and Affymetrix GeneChip miRNA 2.0 Arrays: An Evaluation of Platform Performance

摘要

Genome-wide miRNA level profiling platforms can be applied to measure aberrant post-transcriptional gene regulation in human diseases including cancer. To determine the relative miRNA abundance in paired total RNA samples from tumors and normal tissues from patients with aristolochic acid nephropathy (AAN) with upper urinary tract urothelial carcinomas (UUCs), we performed a systematic performance comparison between two prominent platforms: 1) the high-capacity quantitative PCR using Applied Biosystems megaplex RT primer pools for 754 human miRNAs from the miRBase v14 contents, analyzed by the microfluidics TaqMan Low Density Arrays (TLDA)) and 2) the semiquantitative Affymetrix GeneChip miRNA 2.0 arrays that cover 100 % miRBase v15 contents, with multi-species coverage corresponding to miRNAs of 131 organisms detected by 15,644 probe sets. Systematic data analysis of the TLDA results revealed a signature of 50 miRNAs differentially modulated (19 elevated and 31 reduced) in tumors versus unaffected tissues detected at a reasonable Pearson correlation by both profiling platforms, while there were also platform-specific discrepancies, especially when relative levels and the rank of all human miRNAs were compared. We conclude that for miRNA abundance profiling studies, the performance of these platforms is considerably comparable and we also address the possible sources of observed discrepancies. Next, we discuss the utility of the additional information provided by the broader Affymetrix array content such as the value of cross-reactivity among orthologous probes for non-human species and the value of additional probes for snoRNAs and scaRNAs and most importantly the extensive sets unique to pre-miRNA hairpins. Our study can serve as a useful starting point for specific platform recommendations offered to clients by a genomics shared resource laboratory. Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities.