Cloud-based qPCR analysis software for rapid-throughput screening of antisense oligonucleotides
Recorded On: 02/05/2018
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.
I have over 20 years of biotech software experience in both academic and industry settings. I began my career at Molecular Simulations Inc (now Biovia) developing bioinformatics tools before the first draft of the Human Genome. After a short diversion in the aviation industry, I returned to bioinformatics as a developer at the Protein Data Bank where I created and managed some notable projects including the ImmersivePDB; highlighted in the book “Advances in Computers” by Marvin Zelkowitz. I joined the Research Bioinformatics Department at Genentech (gRED) in 2010 and managed multiple software projects for core labs including research pathology and next-generation sequencing. In 2013 I accepted a position at Ionis Pharmaceuticals where I currently lead software development for the Drug Discovery department. My current focus is in-silico oligonucleotide drug design and software to support high-throughput in-vitro screening.