qNPA™ Excels in Formalin Fixed
Paraffin Embedded (FFPE) Tissue.
qNPA technology is uniquely suited to measure gene expression in FFPE and similar samples where the RNA is not intact or is insoluble. Traditional RNA extraction methods used with FFPE samples can only recover the RNA which is readily soluble, leading to low yields and incomplete recovery. The qNPA approach removes the RNA extraction step, and measures both the soluble and the cross-linked RNA found in FFPE samples directly in the Lysis Buffer. qNPA technology achieves superior, reproducible results, and uses less of your precious FFPE samples to generate more data.
RNA degradation is a common problem in archived samples such as FFPE. This degradation occurs due to a combination of the chemicals used in the tissue fixing process and the effects of moisture and oxygen over time. As a result, the RNA is broken into pieces, of which only a small number contain a poly(A) tail.
Many gene expression analysis techniques involve a cDNA synthesis step which is primed with poly d(T) oligonucleotides. In FFPE samples, the degraded nature of the RNA causes cDNA to be synthesized from only a small portion of the RNA fragments; the majority of the transcript cannot be reverse transcribed. This results in low amplification yields, extreme 3’ bias in the coverage of the specific gene, and generally poor performance in most gene analysis applications.
The qNPA ArrayPlate platform does not require the cDNA synthesis step, and is therefore not subject to many of the problems experienced in other gene expression processes. The qNPA library oligonucleotides can be placed throughout the gene’s sequence with the knowledge that they will successfully hybridize with the RNA present even if the RNA is compromised. In addition, unlike most other methods, the qNPA ArrayPlate does not require an extraction or deparaffinization of the starting material; scraping a small portion of a slide mount into our Lysis Buffer produces excellent results on our standard ArrayPlate platform.
