We do not foresee major difficulties to the prediction of independent samples using the gene signature, provided the same expression quantification technology is used (Affymetrix GeneChip©).
It is also important to note that several different technologies are used for miRNA expression quantification apart from RT-qPCR, e.g. hybridization-based arrays and sequencing technologies [ 33], and our findings may not be applicable to all such technologies.
The application of next-generation sequencing technology to gene expression quantification analysis, namely, RNA-Sequencing, has transformed the way in which gene expression studies are conducted and analyzed.
We assessed the ability of this technology for mRNA expression quantification in archived formalin-fixed, paraffin-embedded (FFPE) oral carcinoma samples.
Based on our results, we conclude that both technologies are useful for gene expression quantification in fresh-frozen or FFPE tissues; however, the probe-based NanoString method achieved superior gene expression quantification results when compared to RQ-PCR in archived FFPE samples.
Gene expression was assessed by Real Time-PCR using an ABI Prism® 7000 Sequence Detection System and TaqMan® technology suitable for relative gene expression quantification as described in Materials and Methods S1.
Expression was assessed by real-time PCR using the LightCycler® 480 Real-Time PCR System (Roche Diagnostics, Barcelona, Spain) and TaqMan® technology suitable for relative gene expression quantification.
Gene expression was assessed by real-time PCR using the LightCycler® 480 Real-Time PCR System (Roche Diagnostics, Barcelona, Spain) and TaqMan technology suitable for relative gene expression quantification following manufacturer's protocol.
Our goal was to determine whether this technology could be applied for accurate gene expression quantification using archived, FFPE oral cancer tissues.
Recently, two array-based technologies, cDNA and oligonucleotide arrays, have been applied to gene expression quantification.
