RNA Detection Technologies

With the increasing importance of molecular diagnostics in the detection of disease and monitoring of treatment, there is a crucial need for detection technologies that can be incorporated into existing diagnostic schemes and overcome the inadequacies of current methods. SomaGenics has developed two technology platforms that address important aspects of diagnostic detection of both mRNA and small RNA molecules.


miR-ID® microRNA Detection Platform

MicroRNAs (miRNAs) are of increasing interest as potential biomarkers and drug targets. SomaGenics is developing novel methods for detecting and quantifying levels of miRNAs in cells and tissues. These methods, which can be applied to all small regulatory RNAs, provide significant improvements over alternative methods.

miR-ID® is a novel platform for detecting miRNA, with no reliance on previous miRNA detection methods. It provides better sensitivity, specificity, and versatility than competing methods, and at a lower cost. In addition, miR-ID is the only PCR based platform to distinguish small RNAs with commonly occurring end modifications. These modifications include 5' triphosphates (found, for example, on secondary siRNAs in C. elegans), and particularly 2'-OMe (found, for example, at the 3' ends of piRNAs in animals and all small RNAs in plants). 2'-O-methylation is thought to play a role in both the stability and function of small RNAs, and there is a clear need for the ability to both detect these modified small RNAs and to differentiate them from their unmodified versions. Currently available platforms lack this capability.

Comparison of miR-ID and the leading competitor for small RNA detection


Sensitivity

The miR-ID miRNA detection platform provides a higher signal-to-noise ratio than the leading competitors, while using unmodified DNA primers, single-fluor detection (SYBR green or EVA green), and no specialized probes. These features also help keep costs low and allow rapid development of assays for miRNAs of interest.

Figure 1: qPCR detection of lin-4 by miR-ID and the leading competitor.
 

Specificity

miR-ID provides unmatched discrimination between miRNA isoforms with single nucleotide differences. There is virtually no cross-talk between miRNAs from the same family, as well as superior discrimination between pre- and mature miRNAs.

Figure 2: miR-ID provides exceptional discrimination of let-7 isoforms
 

Quantification of End-Modified Small RNAs

miR-ID is the first platform that can quantitatively discriminate between small RNAs with the same sequence but differing terminal modifications. This is particularly useful in plant miRNAs, where discrimination between O-Methyl modified and unmodified miRNA is of considerable interest.

Figure 3: miR-ID is able to quantitatively detect 3' O-Methyl modification
 

Convenience

miR-ID can accommodate a variety of RNA sources without purification, including tissue or cell lysates. Where extracts of total RNA are to be analyzed, no enrichment for small RNAs is needed: miR-ID works as well with total RNA as with enriched fractions. To enable point-of-care diagnostic assays without the need for expensive and cumbersome thermo-cyclers, an isothermal variant of miR-ID is in development.


Products in development

  1. Kits for preparing unbiased small-RNA (or fragmented RNA) libraries for next-generation sequencing
  2. Kits for preparing libraries greatly enriched in small RNAs containing 2'-O-methy modifications at their 3' ends
  3. Quantification of highly fragmented mRNAs isolated from formaldehyde-fixed, paraffin-embedded tissue specimens
  4. RNA target enrichment for re-sequencing by RNA-seq