1:00 Chairperson’s Remarks

Dawn Casey, Director, Business Operations, Paragon Genomics

1:05 COVID-19 High Throughput Detection and Surveillance Solutions from Paragon Genomics Using Massively Parallel Sequencing

Lily Liu, Technical Application/Operations Manager, Paragon Genomics

Paragon Genomics was one of the first to develop and commercialize a targeted sequencing panel for SARS-COV-2 genome to support global efforts in COVID-19 coronavirus research. The team was able to quickly develop this SARS-COV-2 targeted panel based on Paragon’s highly sensitive multiplex PCR CleanPlex® technology. The NGS panel is strategically designed to specifically and selectively amplify the full SARS-COV-2 viral genome for confident detection, surveillance, and epidemiology studies. Since its launch in March, the panel has made its way into labs all around the world. In this webinar, we will explore more about the rapid, easy-to-use, ultra-high multiplex PCR-based Target enrichment solution for Next-Generation Sequencing (NGS), and how our proprietary CleanPlex background-removing technology can enable your lab to generate accurate and sensitive data, easily, quickly, and cost-effectively.

1:25 SARS-CoV-2 Sequencing and Genomic Epidemiology Studies

Xiaowu Gai, PhD, Associate Professor, Clinical Pathology, Keck School of Medicine, University of Southern California; Director, Bioinformatics, Center for Personalized Medicine, Children's Hospital Los Angeles

Jennifer Dien Bard, PhD, Associate Professor, Pathology (Clinical Scholar), Keck School of Medicine, University of Southern California; Director, Clinical Microbiology and Virology Laboratories, Children’s Hospital Los Angeles

Since the launch of the SARS-CoV-2 RT-PCR assay on March 13th, the Clinical Virology and Microbiology laboratory at Children’s Hospital Los Angeles (CHLA) has tested over 16,000 specimens. Shortly after, and on March 26th, the CHLA Center for Personalized Medicine launched the full-genome SARS-CoV-2 sequencing research assays in collaborations with Paragon Genomics and Thermo Fisher Scientific. On the informatics side, we quickly established the CHLA COVID-19 Analysis Research Database (CARD), which is a resource for rapid SARS-CoV-2 genome identification using interactive online phylogenetic tools. CHLA CARD is a freely available genomic resource (https://covid19.cpmbiodev.net/). Detailed descriptions of CHLA CARD can be found in the bioRxiv preprint, published on May 11, 2020. With the genomic and informatics tools, we were able to solve the likely transmission patterns of multiple clusters of infections at our hospital. On the research side, genomics epidemiological studies using these genomic and informatics tools: 1) elucidated clear state-specific SARS-CoV-2 haplotypes that showed spatially and temporally localized transmission patterns that pointed to the effectiveness and importance of travel restrictions (medRxiv 2020.05.23.20110452); 2) revealed viral genetic diversity that potentially correlated to clinical exemplifications in pediatric COVID-19 patients (medRxiv 2020.05.28.20104539). We are currently pursuing large genomic epidemiology studies that are coupled with our safe return-to-work testing strategies, and also that involves major children’s hospitals across the nation. Together, we strive to make significant contributions to the containment, management, and treatment of this devastating pandemic not only locally, but nationally and internationally. For this, our SARS-CoV-2 full-genome sequencing and informatics tool sets are the indispensable parts with increasing significance.

1:55 Q&A

Speaker Biographies

Dawn Casey
Director, Business Operations, Paragon Genomics

Dawn Casey is the Director of Business Operations at Paragon Genomics. She has 20 years of Biotech industry experience working for the leading companies in the DNA Sequencing space. Dawn started as a scientist in the lab where she spent her time successfully building and optimizing both high throughput and low throughput pipelines for service providers. She moved to the commercial side of industry 15 years ago to utilize her strong background in operations and lab management to successfully navigate companies through the transition of NGS implementation. Dawn received her Molecular Biology degree from Bridgewater State University, Massachusetts, and is passionate about leading start-up companies to commercial success.

Lily Liu
Technical Application/Operations Manager, Paragon Genomics

Lily Liu has grown with Paragon Genomics since the early days initially as a R&D scientist to now heading the Technical Support and Applications team. Lily received her Chemical Biology degree from University California, Berkeley, and has 8 years of assay development and technical operations experience. She loves the goal-driven start-up environment and enjoys the challenges that come with it.

Xiaowu Gai, PhD
Associate Professor, Clinical Pathology, Keck School of Medicine, University of Southern California; Director, Bioinformatics, Center for Personalized Medicine, Children's Hospital Los Angeles

Dr. Xiaowu Gai is a genomicist and a bioinformatician. Dr. Gai has been co-leading the international Mitochondrial Disease Sequence Data Resource Consortium (MSeqDR) (https://mseqdr.org/) since 2012. He serves a Co-Chair for the ClinGen “Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel” and “Mitochondrial Disease Gene Curation Expert Panel.” Currently, he is an Associate Professor of Clinical Pathology at the Keck School of Medicine of USC, and the Director of Bioinformatics at the Center for Personalized Medicine (CPM) at Children's Hospital Los Angeles (CHLA). The CHLA CPM develops and implements a variety of genomics-based tests for both pediatric cancers (e.g., OncoKids®) and constitutional disorders (e.g., Clinical Exome Sequencing), for which Dr. Gai is responsible for the informatics solutions, following strictly AMP/ACMG guidelines. Most recently, Dr. Gai has been leading the development of genomic and informatics solutions for COVID-19 diagnosis and genomic epidemiology studies at CHLA CPM.

Jennifer Dien Bard, PhD
Associate Professor, Pathology (Clinical Scholar), Keck School of Medicine, University of Southern California; Director, Clinical Microbiology and Virology Laboratories, Children’s Hospital Los Angeles

Dr. Jennifer Dien Bard is the Director of the Clinical Microbiology and Virology Laboratories at Children’s Hospital Los Angeles (CHLA) and Associate Professor of Pathology with Clinical Scholar designation at the University of Southern California Keck School of Medicine. Dr. Dien Bard’s research interests include studying the application of rapid diagnostics in the clinical setting to determine clinical utility. She has authored more than 50 scientific peered-reviewed publications and is a frequent speaker on the topics of rapid diagnostics for infectious diseases. Dr. Dien Bard serves as a member of the professional development committee for ASM and economic affairs committee for AMP and is on the editorial board of the Journal of Clinical Microbiology. Dr. Dien Bard has led the current SARS-CoV-2 RT-PCR testing initiative at CHLA.