Thursday, October 3 • 4:15pm - 4:35pm
Data Automation- Increasing Sequencing Throughput By Making Robots Work Harder, But Always Checking Their Work

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Increasing Sequencing Throughput By Making Robots Work Harder, But Always Checking Their Work
Next-generation sequencing cost declines and capacity increases for the first time make possible high-replicate genome-wide gene expression profiling during drug discovery. This makes library-creation, rather than sequencing, a limiting factor in data generation. The reagent and time costs of sequencing library creation, along with substantial data processing requirements, must be combated with infrastructure to process and analyze more samples. Miniaturization, multiplexing, and automation -- both mechanical and computational -- enable us to process an order of magnitude more samples than benchtop approaches, at nearly half the cost per sample. However, to guarantee robust data at scale, we require careful precautions, randomizations, and embedded controls to spot systematic and sporadic errors. We pre-process samples using Python scripts to organize complex studies with double-barcoding, allowing for pseudo-randomization and integration of controls from the very first step. Our process takes advantage of robotic plate control and both acoustic and displacement liquid handlers. Fully implemented, our process can generate over 2000 sequencing libraries per week.

Co-Author: Sagar Damle, PhD

avatar for Steven Kuntz, PhD

Steven Kuntz, PhD

Sr. Scientist, Ionis Pharmaceuticals
Steven Kuntz conducts sequencing library creation, analysis, and protocol development at Ionis Pharmaceuticals in support of Functional Genomics and Drug Discovery. He received his PhD working on the robustness of muscle differentiation networks in the labs of Barbara Wold and Paul... Read More →


Jeff Milton

Associate Director, Ionis Pharmaceuticals
Jeff Milton has over 20 years of bioinformatics and software development experience in both academic and industry settings. He began his career at Molecular Simulations Inc (now Biovia) developing bioinformatics tools before the first draft of the Human Genome. In 2005 he moved to... Read More →

Thursday October 3, 2019 4:15pm - 4:35pm
Theater Ballroom (5th Fl) - Courtyard Boston Downtown 275 Tremont Street, Boston, MA 02116