Data Analysis and Informatics

Cloud-based qPCR analysis software for rapid-throughput screening of antisense oligonucleotides

• DM

  Donald Milton

  Assistant Director, Antisense Drug Discovery
  Ionis Pharmaceuticals

One distinct advantage of the antisense oligonucleotide (ASO) platform has over other therapeutic approaches is the ability to rapidly screen for safe and effective ASO compounds against new molecular targets. While RNA screening assays will often utilize sequencing technology like RNA-Seq, today, the gold standard for rapid and cost effective gene expression quantification remains quantitative polymerase chain reactions (qPCR). Advances in automation, miniaturization and microfluidics have enabled researchers to develop high-throughput qPCR assays that generate thousands of data points per day creating an increased burden on downstream data management, computation and analysis.

Here we present a software tool to complement these high-throughput methods by simplifying the computation and visualization of screening results for standard-curve experiments. Our qPCR pipeline uses modern cloud technology provided by Amazon Web Services to permit users to dynamically generate workflows for a vast array of plate-based qPCR assays. Our visualization tools make use of the HELM notation (Hierarchical Editing Language for Macromolecules) to both visualize the genomic targets as well as the distinct chemistries employed in SAR screens.