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Professor in Microbial Evolutionary Genomics, University of Birmingham
Infectious Disease Lead for the Milton Keynes Lighthouse Lab UK

Professor of Medicine at KU Leuven, Department of Microbiology and Immunology, Co-Director Infectious Diseases Centre
University Hospital of Leuven

Senior Medical Director
Thermo Fisher Scientific

Viruses mutate as they strive to thrive in response to selective pressures. For molecular diagnostic assays to serve in the management of viral transmission, they need to be designed anticipating the emergence of mutations.

This webinar will focus on the impact of emerging viral variants of SARS-CoV-2 on molecular diagnostic testing. In the first part of the session, Dr. Alan McNally will share how the B.1.1.7 variant was discovered in the United Kingdom, highlight the role played by a molecular diagnostic assay in its detection, and discuss design principles that aid in the development of effective and robust molecular diagnostic assays. In addition, Dr. McNally will discuss some of the clinical data associated with the B.1.1.7 strain as well as the importance of early identification of this variant of concern.

In the second part of the session, Dr. Emmanuel André will discuss his approach to identifying specific SARS-CoV-2 variants using a targeted mutation panel as a reflex test following a suspect clinical variant result. Dr. Andre will provide details about the mutation panel composition as well as the advantages of using this approach for wide-scale SARS-CoV-2 surveillance.

Learning Objectives:

  • Hear the story of detecting the B.1.1.7 variant (UK variant) from a world-leading epidemiologist.
  • Understand the importance of early detection of viral variants and the impact of emerging variants on global response efforts.
  • Learn about molecular diagnostic assay design principles to safeguard against unexpected false results due to mutations and the means to monitor assays as early indicators of emerging variants.
  • Learn about the S-gene advantage with B.1.1.7, the role of the S-gene dropout, and the value of a targeted mutation panel as a reflex tool as follow up for a suspected clinical variant.
Sponsored by
GenomeWebinar

Postdoctoral Fellow, Department of Pathology
Stanford University School of Medicine

Metabolism drives cell behavior, including immune cell activation, differentiation, and effector functions. However, current technologies for the analysis of cellular metabolism lack single-cell resolution and simultaneous characterization of cellular phenotype.

In this webinar, Felix J. Hartmann of Stanford University will describe an approach that characterizes the metabolic regulome of individual cells together with their phenotypic identity. The method, termed single-cell metabolic regulome profiling (scMEP), quantifies proteins that regulate metabolic pathway activity using high-dimensional antibody-based technologies. Dr. Hartmann and colleagues employed single-cell approaches to benchmark scMEP against bulk metabolic assays by reconstructing the metabolic remodeling of in vitro-activated naive and memory CD8+ T cells.

Combining this method with multiplexed ion beam imaging by time of flight (MIBI-TOF), Dr. Hartmann’s team uncovered the spatial organization of metabolic programs in human tissues, which indicated the existence of metabolic niches and exclusion of metabolically repressed immune cells from the tumor–immune boundary.

Dr. Hartmann will discuss how this approach enables robust approximation of metabolic and functional states in individual cells and tissues.

Sponsored by
Partner Webinar

FFPE tissue and samples with a low abundance of high-quality nucleic acid represent a bottleneck in sample preparation workflows. Researchers and clinicians working with these samples often resort to labor-intensive and potentially biased methods in order to isolate sufficient material for downstream analyses.
Purigen’s Ionic Purification System uses isotachophoresis to separate and concentrate DNA and RNA in solution solely based on their electrophoretic mobility. Biological samples are gently lysed and added to the Ionic Fluidic Chip. An electric field is then applied to the chip and the nucleic acid is isolated in its natural, native form. The nucleic acid is not denatured or dehydrated, and there’s no binding to, or stripping from, fixed surfaces. The result is a higher yield of pure nucleic acid that is less fragmented and free from bead or wash buffer contamination. The new Ionic FFPE Complete Purification Kit enables extraction of both DNA and RNA (including miRNA) simultaneously from FFPE samples in a single workflow.
In this webinar, we share results and data (from Purigen and Canopy Biosciences) from downstream molecular analyses of DNA and RNA that was performed with the new Ionic FFPE Complete Purification Kit.

In the webinar you will learn:
• Purigen Biosystems’ innovative approach to automated nucleic acid purfication using isotachophoresis
• How the Ionic Purification System can be used to extract more DNA and RNA from challenging FFPE samples with more reliability and less effort by comparison to conventional extraction methods

Sponsored by
GenomeWebinar

Professor, Microbiology, Immunology & Pathology, Director, Molecular Quantification Core, Director, Cell & Molecular Biology Graduate Program, Colorado State University

Associate Professor, Department of Civil and Environmental Engineering, Colorado State University

Chief Medical Research Officer, Colorado State University

Wastewater based epidemiology (WBE) has been established as a viable, valuable, and cost-effective means to monitor infectious disease within a community. 

In this webinar, a team of scientists from Colorado State University (CSU) will describe their experiences building a successful wastewater surveillance system from the ground up for use as a state-wide system to monitor viral loads in wastewater. 

The CSU team worked with GTMolecular to develop and validate a method to concentrate and extract SARS-CoV-2 RNA from wastewater samples provided by wastewater treatment plants (WWTP) or collected from sewers on the CSU campus. Levels of SARS-CoV-2 are quantified using digital droplet PCR assays.

Using this method, the CSU team tracked trends in viral load over time for 21 Colorado WWTPs and connected this information to the area covered by each WWTP to inform public health decisions. They also monitored SARS-CoV-2 in wastewater from 20 locations, including CSU dormitories and off-campus shared living facilities. 

The CSU scientists will discuss how this micro-surveillance approach allowed scarce testing resources to be allocated where risk was highest, helped detect outbreaks early through directed clinical testing of residents, and identified targets for compliance efforts. 

They will also describe the interface of wastewater surveillance with university and local public health initiatives and speculate as to the future for WBE in detecting and curbing infectious disease outbreaks.

Sponsored by
Partner Webinar

Host immune responses play a central role in controlling SARS-CoV-2 infection, but they remain incompletely characterized and understood.
In this webinar, Dr. Yapeng Su of the Institute for Systems Biology will present an integrated analysis of the clinical measurements, immune cells, and plasma multiomics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis.
As recently published in Cell, Dr. Su’s team identified a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity.
Dr. Su and colleagues condensed more than 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease.
This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.

Sponsored by
March 11, 2021
Sponsored by
Foundation Medicine

Virtual Molecular Tumor Board Series: Gene Fusions as Druggable Targets

GenomeWebinar

Medical Director, Precision Medicine
Geriatric Oncology Consortium

Chief, Precision Health and Genomics
Intermountain Healthcare

Research Scientist, Personalized Medicine Specialist,
DeBartolo Family Personalized Medicine Institute, H. Lee Moffitt Cancer Center

Co-Director, Oncology Precision Medicine Program,
Aurora Health Care

Lead Variant Scientist,
Intermountain Healthcare

In this session, the third in the Precision Oncology News Virtual Molecular Tumor Board Series, our expert panelists will review patient cases in which genomic profiling has identified gene fusions that may or may not serve as druggable targets.

Precision medicine has been focused on the presence of activating mutations or gene amplifications. However, recent data has shown that the presence of gene fusions also offer a unique treatment opportunity, with the potential for durable clinical responses.

Our panel will discuss several such clinical cases in detail and recommend a course of treatment based on the genomic profiles of the patients.

The session will wrap up with a live Q&A in which attendees can discuss the cases with the Virtual Molecular Tumor Board panelists.

About The Series

The Virtual Molecular Tumor Board Series is an interactive and educational online program intended to highlight the key role that molecular tumor boards play in implementing precision oncology.

The series will underscore the collaborative nature of genomic medicine by assembling a multidisciplinary panel of experts who will meet virtually for four one-hour sessions. In each session, the panel will review the genomic and clinical evidence for anonymized patients who have had their tumors sequenced as part of clinical management. The panel will discuss each case and recommend a course of treatment.

Precision Oncology News would like to thank Clariifi for assistance in planning and executing this educational webinar series.

Sponsored by
GenomeWebinar

Director, Laboratory of Genetics and Genomics, Division of Human Genetics,
Associate Professor, UC Department of Pediatrics

Bioinformatician,
Cincinnati Children’s Hospital Medical Center

Scientist,
Fabric Genomics

The growth of next-generation sequencing (NGS) testing presents both opportunities and challenges for clinical, informatics, and laboratory teams. This webinar discusses best practices and lessons learned for implementing and scaling whole-exome and virtual panel testing at Cincinnati Children’s Hospital Medical Center. This includes both clinical considerations as well as end-to-end integration with the lab’s laboratory information management system (LIMS) as well as the hospital’s Epic Beaker laboratory information system (LIS) for seamless workflow and regulatory compliance.

In this webinar, you will learn:

  • Tips for integrating an artificial intelligence interpretation platform with a lab LIMS and hospital LIS
  • Best practices for optimizing diagnostic yield and turnaround time
  • First look at the benefits of Fabric AI
Sponsored by
GenomeWebinar

Laboratory Head
IMD Labor Frankfurt

Biologist
Seq-IT

Vice President, Scientific Affairs
Agena Bioscience

As new variants of SARS-CoV-2 circulate around the globe, there is growing concern among clinical laboratories that these variants may impact their ability to accurately detect the virus.  Understanding the impact of these variants on molecular testing methods and how labs can address this added complexity is important to managing the diagnostic response to the ongoing pandemic.

In this webinar Dr. Martin Stürmer of IMD Labor Frankfurt will discuss the effects of emerging SARS-CoV-2 variants on diagnostic methods and the clinical utility of detecting and discriminating them. Thomas Alef of Seq-IT will then present how his clinical lab was able to react to the emergence of new, often more contagious, variants of the virus by rapidly designing a highly multiplexed SARS-CoV-2 variant panel using the low-cost, high-throughput MassArray System from Agena Bioscience.

Sponsored by
GenomeWebinar

Medical Director, Precision Medicine;
Geriatric Oncology Consortium

Chief, Precision Health and Genomics,
Intermountain Healthcare

Research Scientist, Personalized Medicine Specialist,
DeBartolo Family Personalized Medicine Institute, H. Lee Moffitt Cancer Center

Co-Director, Oncology Precision Medicine Program,
Aurora Health Care

Lead Variant Scientist,
Intermountain Healthcare

In this session, the second in the Precision Oncology News Virtual Molecular Tumor Board Series, our expert panelists will review cases in which patient genomic profiles exhibit common driver mutations in tumor types considered “off label” for targeted therapies associated with those mutations.

US Food and Drug Administration approvals for targeted anticancer therapy are most often for specific types of cancer that possess specific driver mutations. However, the broad application of comprehensive genomic profiling has identified the presence of potential “druggable” driver mutations in malignancies for which FDA approval is not yet obtained.

Our panel will discuss several such clinical cases in detail and recommend a course of treatment based on the genomic profiles of the patients.

The session will wrap up with a live Q&A in which attendees can discuss the cases with the Virtual Molecular Tumor Board panelists.

About The Series 

The Virtual Molecular Tumor Board Series is an interactive and educational online program intended to highlight the key role that molecular tumor boards play in implementing precision oncology.

The series will underscore the collaborative nature of genomic medicine by assembling a multidisciplinary panel of experts who will meet virtually for four one-hour sessions. In each session, the panel will review the genomic and clinical evidence for anonymized patients who have had their tumors sequenced as part of clinical management. The panel will discuss each case and recommend a course of treatment.

Precision Oncology News would like to thank Clariifi for assistance in planning and executing this educational webinar series.


Sponsored by
GenomeWebinar

Director, Strategy and Business Development,
Qorvo Biotechnologies

VP Business Development,
Schott Minifab

Developing a fully integrated consumable cartridge for an automated diagnostic platform is a significant challenge. More challenging still is developing such a cartridge in response to a deadly global virus pandemic amid market uncertainty and extraordinary time constraints. 

This has been the case with the development and quick manufacturing scaleup of Qorvo's COVID-19 test. Primary among these challenges has been acquiring and coordinating broad multidisciplinary expertise among Qorvo’s team of people and partners; successfully cultivating the capabilities and culture to be flexible and innovative in face of extreme uncertainty; and, lastly, developing access to broad manufacturing scalability to accommodate the flexibility needed from product development to high-volume manufacturing.

This webinar will present a case study outlining Qorvo's path in developing and commercializing its COVID-19 test. In so doing, participants can expect to learn:

  • Key challenges of diagnostic test development, both anticipated and unanticipated
  • Relevant factors during development that are important to eventual successful commercialization
  • Perspective on the need for development and manufacturing partners and what capabilities they should possess.
Sponsored by
February 23, 2021
Sponsored by
Thermo Fisher Scientific

After the Surge: Driving Sample Processing Efficiency of Coronavirus Samples

GenomeWebinar

R&D Scientist IV,
ARUP Laboratories

Director, Clinical Product Development, Thermo Fisher Scientific

As the world continues to contend with coronavirus and a surge in the infection rate, labs are required to run more samples than ever before. Labs face new challenges such as having to process large volumes of samples with a quick turnaround time, the constant risk of falling into backlog, and the possibility of loss of reimbursement (for certain samples). But what happens after the surge, when infection rates decline but testing will still be a necessary component of managing the virus? 

During this presentation, Weston Hymas of ARUP Laboratories will discuss the clinical validation of a SARS-CoV-2 sample pooling protocol that can be used to exponentially increase testing efficiency, enabling a higher volume of sample processing in lower prevalence rate populations. This method can be implemented by clinical labs for routine processing of samples from populations with low infection rates. 

Sponsored by
Partner Webinar

Clinical Molecular Geneticist
University Health Network

Development Technologist II and Assistant Professor in the Genomics Laboratory, Mayo Clinic

VP of Clinical Product Management and Marketing, Qiagen

Technical Director,  Pangaea Oncology; Quiron Dexeus University Hospital

Please join GenomeWeb and Qiagen for an on-demand roundtable discussion where a panel of experts reviews challenges and opportunities around genomic variant interpretation workflows in the field of oncology.

Recently, GenomeWeb and Qiagen partnered on a survey that allowed participants to assess their oncology variant interpretation workflows. This webinar presents the results of the survey and offers an interactive environment for clinical labs to assess their own variant interpretation capabilities.

The discussion covers a range of capabilities related to variant interpretation workflows, including:

  • Resources and skills
  • Workflow optimization
  • Variant interpretation content knowledge.
Sponsored by
GenomeWebinar

Associate Professor,
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center

The composition of the immune infiltrate in the human tumor microenvironment is a critical determinant of disease progression. However, it has been unclear how tumor-specific inflammatory processes relate to inflammation in non-malignant tissues.

This webinar will discuss a single-cell study that compared the immune landscape of human head and neck squamous cell carcinoma (HNSCC) in the oral and oropharyngeal cavity to inflamed oral mucosal tissue samples, in an effort to identify tumor-unique immune alterations.

Dr. Martin Prlic of the Fred Hutchinson Cancer Research Center will share details of the project, which found a considerable phenotypic congruence of immune cells in inflamed versus tumor tissues, including the presence of T cells with an exhausted phenotype as well as recently described mature dendritic cells enriched in immunoregulatory molecules (mregDCs).

Computational and machine learning analyses revealed previously unidentified tumor-unique immune subsets and signaling axes, while experimental validation confirmed a tumor-unique subset of regulatory T cells (Tregs).

Attendees of this webinar will learn:

  • How cutting-edge single-cell techniques are used to study the microenvironment in human tissue samples
  • Insights into the immune alterations in the human tumor microenvironment
  • A blueprint for a novel discovery approach of immunotherapeutic targets in the human tumor microenvironment
Sponsored by
February 16, 2021
Sponsored by
Thermo Fisher Scientific

Differentiate DNA from RNA using NanoDrop Spectrophotometers

Partner Webinar

The similarity of absorbance spectra between DNA and RNA makes typical UV-Vis analysis less effective at distinguishing the two nucleic acids. It results in a greater risk of spending time and resources on downstream measurements only to find that the DNA sample was contaminated with RNA or vice versa. The researcher shoulders the responsibility of ensuring sample purity at the start for success down the line. 

This 13-minute video reviews how absorbance is used to analyze nucleic acid samples. It also shows how modern UV-Vis spectrophotometer software using chemometric modeling can detect DNA/RNA contamination in samples and provide corrected concentrations.

Sponsored by
Partner Webinar

Senior Research Scientist in the Regev Lab,
Broad Institute of MIT and Harvard

Application Scientist, Advanced Cell Diagnostics 

This on-demand webinar discusses a project at the Broad Institute to use spatial profiling to understand the disease progression of COVID-19. 

Sami Farhi of the Broad Institute shares details of the project, which performed transcriptomic and proteomic spatial analysis on lung parenchyma from rapid autopsies of patients succumbing to the disease. 

The team used NanoString GeoMx to perform whole-transcriptome, cancer transcriptome, and protein studies on 17 donor samples. More than 12 regions of interest were selected for each donor, guided by RNAScope against the SARS-CoV-2 S gene to identify regions of high and low viral load. 

Farhi and colleagues performed differential analyses of epithelial and non-epithelial compartments across different viral load, anatomical compartment, and inflammation status. Results matched conclusions from single-cell and bulk RNA sequencing data on the same samples. 

Dr. Farhi discusses how the study highlights the utility of RNAScope in guiding other spatial analysis methods as well as how the data set captures the intra- and inter-sample expression heterogeneity associated with COVID-19, highlighting both early response mechanisms to SARS-CoV-2 and subsequent late-stage responses to viral damage.

Key Learning Points:

  • Spatial variation of gene expression programs in COVID-19 tissues
  • Guiding Nanostring GeoMx experimental design with RNAScope measurements
Sponsored by

Pages

A small, early-stage trial of a combination therapy for brain cancer reports favorable responses in two patients, according to the Guardian.

Nature News writes that viral genomic surveillance in the US faces systemic issues.

President Joe Biden is seeking an increase in federal spending, including higher budgets for the National Institutes of Health and Centers for Disease Control and Prevention.

In PLOS this week: sex-stratified genome-wide association study of chronic pain, sequencing data from Indigenous Mexican groups, and more.

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