Cross-platform analysis of global microRNA expression technologies.
BACKGROUND
Although analysis of microRNAs (miRNAs) by DNA microarrays is gaining in popularity, these new technologies have not been adequately validated. We examined within and between platform reproducibility of four miRNA array technologies alongside TaqMan PCR arrays.


RESULTS
Two distinct pools of reference materials were selected in order to maximize differences in miRNA content. Filtering for miRNA that yielded signal above background revealed 54 miRNA probes (matched by sequence) across all platforms. Using this probeset as well as all probes that were present on an individual platform, within-platform analyses revealed Spearman correlations of >0.9 for most platforms. Comparing between platforms, rank analysis of the log ratios of the two reference pools also revealed high correlation (range 0.663-0.949). Spearman rank correlation and concordance correlation coefficients for miRNA arrays against TaqMan qRT-PCR arrays were similar for all of the technologies. Platform performances were similar to those of previous cross-platform exercises on mRNA and miRNA microarray technologies.


CONCLUSIONS
These data indicate that miRNA microarray platforms generated highly reproducible data and can be recommended for the study of changes in miRNA expression.
Yauk
Carole L
CL
Environmental Health Sciences and Research Bureau, Health Canada, Ottawa, ON, Canada. Carole_Yauk@hc-sc.gc.ca
Rowan-Carroll
Andrea
A
Stead
John Dh
JD
Williams
Andrew
A
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019914:Taq Polymerase / Q000378:metabolism
D035683:MicroRNAs; D019914:Taq Polymerase