jarmstropreamp

Our goal is to add additional markers to current candidates using our enrichment tech. It helps to remember that up until the ILMN/Solexa machine came online around 2005-6, we could not reliably detect (statistically) MAFs in heterogenous tumor samples below about 20% on the 454 platform (depending on how much cash you threw at the sample). Point is, our enrichment platform allows a deep dive into signals that have yet to be identified as reliable and low variance biomarkers.

The work with these molecules is early enough, that to my knowledge, there are no studies of this type that are published. And, in fact one could pose the same question for linear mRNA and ncRNA in exosomes (or ESVs). Most of the studies are on miRNA in ESVs, however we have done considerably work internally on characterizing long- mRNA and ncRNA in exosomes. These vesicles are fascinating!

Jonlucc, Shoot us an email through the website and I am sure we can set something up.

Hi daemonk, Jon Armstrong from Cofactor Genomics here. You hit on some excellent points.

So you can detect circ. RNA that come from specific tissues and partition those reads out as expression for those tissues?

In reality, we are detecting circRNA that arises or predominates during a specific disease state and then partition those reads out as a signal for the disease state. On a related note, the circRNA molecule resists degradation much more than linear RNA molecules, leading to a longer half-life and less variability in signal from tissue, plasma, and exosomes.

What kind of coverage do you need to do that?

Currently, 100's of million of reads need to be generated to just detect the highest expressed circRNAs. We have a patent pending circRNA enrichment technology (supported by a large NIH phase II grant) that increases the ratio of circRNA in the total RNA pool by logs, thus one could sequence logs less reads for the same level of detection. The coverage cutoff for detection can be "tuned" for assay sensitivity.

Are mRNA circularization rates consistent among different genes?

CircRNAs do not seem to be translated into proteins and probably perform multiple regulatory functions. Also, the level of a linear form does not correlate with the level of the circular form for the same gene. As with linear mRNA production, which is not consistent from gene to gene or tissue to tissue, we observe the same phenomenon with circRNA.

Hope this info helps.