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Next Generation Sequencing Webinar

Automation & Miniaturization of Clinical SARS-CoV-2 RT-qPCR Testing For Population Surveillance

Thursday, 17th December 2020 | 16:00 GMT | 08:00 PT

Presented by-
Louise Laurent, Professor,
UCSD Department of OB/GYN and Reproductive Sciences 
Gene Yeo: COVID-19 individual testing workflow , Professor,
UCSD Department of Cellular and Molecular Medicine 
Rob Knight: COVID-19 wastewater testing program, Professor,
Department of Pediatrics 
Peter DeHoff: Mosquito automation and miniaturization, Project Scientist,
UCSD Department of OB/GYN and Reproductive Sciences

Populations that have controlled COVID-19 to a degree that allows for resumption of near-normal economic and educational activities have all employed a combination of infection control and surveillance activities. Successful surveillance requires sensitive and specific SARS-CoV-2 testing infrastructure that can collect, analyze, and return results for large numbers of samples at low cost with rapid turnaround time.

Here, we present our approach to setting up and operating the UC San Diego EXCITE lab, which employs a highly automated workflow for efficient end-to-end operations from sample collection and accessioning to return of results.

  • Overall significance/utility of frequent surveillance testing for COVID-19, including individual-level and community-level testing
  • Barriers to frequent surveillance testing
  • Setting up the UCSD EXCITE lab with highly automated workflows, including a custom LIMS, for efficient and cost-effective clinical COVID-19 testing
  • Examples of the many different workflows implemented in EXCITE, including nasal swab- and saliva-based individual testing and waste water-based community testing
  • Findings from implementing these workflows to perform surveillance on UCSD students and staff

Louise Laurent, Professor, UCSD Department of OB/GYN and Reproductive Sciences
Dr. Laurent received her medical and doctoral degrees from the University of California, San Francisco, and completed her residency in Obstetrics and Gynecology and her fellowship in Maternal Fetal Medicine at the University of California, San Diego. Her research focuses on using stem cell and genomic approaches to understand early embryo development and normal and complicated pregnancy.

Gene Yeo: COVID-19 individual testing workflow , Professor, UCSD Department of Cellular and Molecular Medicine
Gene Yeo PhD MBA is a Professor of Cellular and Molecular Medicine at the University of California San Diego (UCSD), a founding member of the Institute for Genomic Medicine and member of the UCSD Stem Cell Program and Moores Cancer Center. Dr. Yeo has a BSc in Chemical Engineering and a BA in Economics from the University of Illinois, Urbana-Champaign, a Ph.D. in Computational Neuroscience from Massachusetts Institute of Technology and an MBA from the UCSD Rady School of Management.

Dr. Yeo is a computational and experimental scientist who has contributed to RNA biology and therapeutics. His primary research interest is in understanding the importance of RNA processing and the roles that RNA binding proteins (RBPs) play in development and disease. Since inception, Dr. Yeo’s lab has focused on uncovering molecular principles by which RBPs affect gene expression, how RBP- mediated post-transcriptional gene networks contribute to cellular homeostasis in stem cells and the brain, and how mutations in RBPs lead to human developmental and neurodegenerative disease. His lab pioneered computational algorithms and experimental methods in human disease-relevant systems to conduct systematic and large-scale studies.

Rob Knight: COVID-19 wastewater testing program, Professor, Department of Pediatrics
Rob Knight is the founding Director of the Center for Microbiome Innovation and Professor of Pediatrics and Computer Science & Engineering at UC San Diego. Before that, he was Professor of Chemistry & Biochemistry and Computer Science in the BioFrontiers Institute of the University of Colorado at Boulder, and an HHMI Early Career Scientist. He is a Fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology. He was recently honored with the 2019 NIH Director’s Pioneer Award for his microbiome research. He received the 2017 Massry Prize, often considered a predictor of the Nobel. In 2015 he received the Vilceck Prize in Creative Promise for the Life Sciences. He is the author of “Follow Your Gut: The Enormous Impact of Tiny Microbes” (Simon & Schuster, 2015), coauthor of “Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System (St. Martin’s Press, 2017) and spoke at TED in 2014. His lab has produced many of the software tools and laboratory techniques that enabled high-throughput microbiome science, including the QIIME pipeline (cited over 17,000 times as of this writing) and UniFrac (cited over 7000 times including its web interface). He is co-founder of the Earth Microbiome Project, the American Gut Project, and the company Biota, Inc., which uses DNA from microbes in the subsurface to guide oilfield decisions. His work has linked microbes to a range of health conditions including obesity and inflammatory bowel disease, has enhanced our understanding of microbes in environments ranging from the oceans to the tundra, and made high-throughput sequencing techniques accessible to thousands of researchers around the world.

Peter DeHoff: Mosquito automation and miniaturization, Project Scientist, UCSD Department of OB/GYN and Reproductive Sciences
Dr. DeHoff is expert in performance and automation of molecular assays, including qPCR and NGS library preparation, DNA construct design/cloning, and biochemical fractionation of protein/particles from biofluids. He has applied these skills to biomarker discovery for a variety of diseases, including pregnancy complications such as preeclampsia.

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