Grau M, Sole X, Obrador A, Tarafa G, Vandrell E, Valls J, Moreno V, Peinado MA, Capella G. (2005) Validation of RNA arbitrarily primed PCR probes hybridized to glass cDNA microarrays: Application to the analysis of limited samples.
The majority of archival tumour specimens exist as routinely prepared formalin-fixed and paraffin-embedded tissue (FFPET), which is generally regarded as being unsuitable for microarray applications due to the presence of degraded and chemically modified RNA.
Most microarray applications attempt to assess the relative abundance of individual nucleic acids species by labeling it (along with others in the mixture) directly, in sequence-independent manner [ 14- 17] and [ 18].
To date, however, microarray applications are still limited to preliminary screening of genome-scale transcription profiling or gene ontology analysis.
To this end, the NuGEN WT-Ovation™ Pico RNA Amplification System, which is generally intended for microarray applications, was initially used to generate large amounts of single stranded DNA from a small initial quantity of RNA using a three step process following the manufacturer's instructions.
As a caveat to our approach, while these conditions did not negatively impact on barcode microarray specificity, the suitability of this approach to other microarray applications utilizing longer DNA or RNA targets would need to be assessed.
In many microarray applications careful selection of probes to uniquely match target transcripts can be used to eliminate cross-hybridization biases.
However, for successful microarray applications, several important issues need to be addressed, including (i) selection of representative sets of annotated functional genes, and (ii) specificity of microarray probe hybridization within the context of a large pool of unknown environmental mRNA [22].
However, more precise LOD and LOQ are necessary to expand microarray applications as a detection tool in various research fields.
