(1074-A) Full automated qPCR for small molecule screening of RNA targets

Abstract: qPCR is a quantitative and reliable method to determine endogenous gene expression and alternative splicing levels. To investigate signalling pathways inducing gene expression or splice modifiers we tend to use indirect assays (i.e. reporter assays) for high throughput screening since they are easier to automate and miniaturize. However, many false positive hits are inherent features of these types of screens.

In order to be able to screen on the actual endogenous RNA target on a large number of compounds (>50K) we have optimized and automated a qPCR screening workflow and data analysis.

We have established two different workflow for the pre-qPCR steps, one in a automated manner for regular profiling and small screens for up to 15K compounds/day in single point, and one using a fully automated HTS system for up to 50K compounds/day in single point (150 plates/day). For the qPCR step, the capacity is limited by the number of readers available on the system, whereby up to 20 plates can be processed per machine per day (7K compounds/day). In our current workflow we included enough readers redundancy to process up to 40 plates/day.
Throughput format from manual is only 14 plates/day.

We are currently expanding integrating the qPCR machines fully into the robotic system to reduce hands-on time. With this we plan to expand into new target spaces and use cases after having conducted these successful screens.