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Postdoctoral Research Fellow,
University of Notre Dame

Environmental Scientist,
Hampton Roads Sanitation District

As worldwide COVID-19 cases continue to rise, there is a significant need to increase testing and population surveillance capacity. Traditionally such efforts have relied solely on clinical testing of individual patients. But recent reports demonstrate that a proportion of the individuals infected with SARS-CoV-2, the virus responsible for COVID-19, shed viral RNA into feces providing the opportunity to surveil wastewater to monitor the presence and trends of SARS-CoV-2 infection within a community. This practice, known as wastewater-based epidemiology (WBE), has been previously used to monitor public health status for a number of viruses including poliovirus, norovirus, hepatitis A, hepatitis E, and aichi virus.  Importantly, initial studies indicate that SARS-CoV-2 RNA shedding in feces is agnostic to symptom severity, which indicates WBE could provide less biased public health monitoring than clinical testing alone. 

In this webinar, Aaron Bivins of the University of Notre Dame will describe methods for direct-adsorption extraction and Droplet Digital PCR (ddPCR) for the sensitive and reproducible quantification of SARS-CoV-2 RNA in primary influent samples from two municipalities.  

Raul Gonzalez of Hampton Roads Sanitation District will provide insights on a 20-week study demonstrating that wastewater SARS-CoV-2 concentrations have steadily risen ahead of clinically confirmed cases and propose several ways that data can be presented to be of greatest use to public health officials. 

Together they will highlight the utility of wastewater-based epidemiology to detect and track SARS-CoV-2 infection within a community using Droplet Digital PCR. 

Sponsored by

Vice President, Scientific Affairs, SpeeDx

Senior Field Application Scientist, UgenTec

Business Development Manager, Latin America, Thermo Fisher Scientific

This webinar will present a case study from in vitro diagnostics developer SpeeDx on its experience building a complete sample-to-result workflow — encompassing instrumentation and data analysis software — for its qPCR-based ResistancePlus MG Mycoplasma genitalium assay.

Data analysis software has become an integral component of in vitro diagnostic assays in general, and molecular diagnostic tests in particular. The ability to provide a software solution for end users that accurately reports results, identifies technical issues, and can be integrated with a laboratory’s information systems can be as important in the final decision about whether to adopt a given platform as analytical and clinical performance data.

Another important consideration for molecular diagnostic development is the decision whether to develop a novel instrument or to leverage a third-party open platform. Considerations not only include size or price, but also the global installed base, available service plans, options for instrument placement and reagent rental. These choices impact capital efficiency, time to commercialization, and accelerated adoption of the assay in the market. 

SpeeDx is a developer of innovative multiplexed molecular diagnostic assays that employ a novel PCR technology (PlexZyme). Although the assay chemistry is flexible and instrument agnostic, the company needed a customizable software application that could take unique data feeds from different instruments and turn them into accurate reportable results with minimal involvement from end users.

This presentation will discuss the partnership between SpeeDx and Ugentec to produce an integrated data analysis solution for SpeeDx customers running the assay on the Applied Biosystems 7500 Fast Dx Real-Time PCR Instrument , covering the key elements of the Ugentec software. 

After the main presentation, UgenTec will briefly discuss its FastFinder software platform that allows labs and assay providers to build sample-to-result workflows and Thermo Fisher Scientific will briefly introduce its instrumentation, reagent, and services portfolio for assay development. The presentations will be followed by an interactive Q&A session with attendees.

Sponsored by
Mon
Aug
24
1:00 pm2020
Sponsored by
Genecentric

Utility of Novel RNA-Based Tools in Oncology Drug Development

GenomeWebinar

Director of the Lineberger Bioinformatics Core and Research Associate Professor of Genetics, University of North Carolina at Chapel Hill

Vice President of Discovery and Translational Science, GeneCentric Therapeutics

This webinar, Part 1 of the “Advances in RNA-based Biomarker Development for Precision Oncology” webinar series sponsored by GeneCentric Therapeutics, will discuss how gene expression signatures can accelerate (and rehabilitate) drug programs, define targeted patient populations, expand drug indications, and improve clinical success.

Speakers will detail a range of topics, including how expression-based subtyping can eclipse DNA targeted panel technologies in determining patient’s likely response to treatment; the use of clinical subtypes and custom response signatures to select the right therapy for the right patient to improve treatment responses; and the identification of new tumor types for therapies.

Joel Parker of the University of North Carolina at Chapel Hill will discuss the identification of diverse molecular phenotypes with RNA-seq, focusing on expressed mutations, immune phenotypes, and viral detection and quantification.

Kirk Beebe of GeneCentric Therapeutics will follow with a presentation outlining the use of RNA-seq for bolstering drug development programs by circumventing mutational status and deciphering the functional expression of tumors. In particular, he will discuss how bulk tumor sequencing offers the ability to simultaneously assess diverse members of the tumor microenvironment such as cancer and immune cells and will share details of how this approach has been applied in both targeted and immunotherapies.

Sponsored by

Associate Professor of Pathology,
Harvard Medical School

Postdoctoral Fellow,
Brigham and Women's Hospital

Senior Scientist,
IONpath 

This webinar will discuss how high-definition spatial proteomics, enabled by Multiplexed Ion Beam Imaging (MIBI), can be used to explore the immune microenvironment of tumor biopsy samples, illustrated by a case study at Dana-Farber Cancer Institute.

Dana-Farber Cancer Institute is participating in the Human Tumor Atlas Network, a collaborative project funded by the National Cancer Institute that is constructing three-dimensional atlases of the cellular, morphological, molecular features of human cancers over time. 

 

In this webinar, Scott Rodig of Harvard Medical School will provide an overview of Dana-Farber’s involvement in the Human Tumor Atlas Network and Kyle Wright of Brigham and Women’s Hospital will share a case study, along with validation methods and repeatability metrics. 

The webinar will discuss the role of high-definition spatial proteomics for single-cell phenotype mapping and will review data analysis methods used to generate actionable insights from highly multiplexed, spatial proteomic data. 

Speakers will also share plans for tumor analysis at Dana Farber and the potential future impact of high-definition spatial proteomics for cancer therapeutics.

Sponsored by

Division of Cancer Genome Research,
German Cancer Consortium and German Cancer Research Center

Non-small cell lung cancer (NSCLC) patients with ALK rearrangements are treated with tyrosine kinase inhibitors (TKIs), which often leads to prolonged overall survival. However, treatment resistance will almost inevitably occur, and the disease remains incurable.

The presentation will discuss a recent study addressing the longitudinal genotyping of circulating cell-free DNA (cfDNA) from patients with ALK rearrangements by combining panel-based deep sequencing with shallow whole-genome sequencing.

The results suggest that this liquid biopsy approach might be able to improve the care of ALK-mutated NSCLC patients through early detection of resistance mutations and indications of disease progression.

Sponsored by

Assistant Professor, Neuroscience Department,
Mayo Clinic

 

Alzheimer’s disease is genetically complex with no meaningful therapies or pre-symptomatic disease diagnostics. Most of the genes implicated in Alzheimer’s disease do not have a known functional mutation, meaning there are no known molecular mechanisms to help understand disease etiology. 

In this webinar, Mark T. W. Ebbert of the Mayo Clinic will discuss his team’s work toward identifying functional structural mutations that drive disease in order to facilitate a meaningful therapy and pre-symptomatic disease diagnostic.  

Some of the genes and regions implicated in Alzheimer’s disease are genomically complex and cannot be resolved with short-read sequencing technologies. These regions include MAPT, CR1, and the histocompatibility complex (including the HLA genes). 

Dr. Ebbert will share now the Saphyr system from Bionano Genomics resolves full haplotypes for these complex Alzheimer’s disease regions, as well as regions directly involved in other diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Parkinson’s disease.

Sponsored by
Thu
Aug
27
1:00 pm2020
Sponsored by
Cellecta

CRISPR/Cas9 Screens to Investigate Mechanisms of Cancer Drug Resistance

GenomeWebinar

Post-doctoral research associate, Memorial Sloan Kettering Cancer Center 

Chief Operating Officer, Cellecta, Inc.

Over 70 percent of breast cancers are estrogen receptor positive and are treated with endocrine therapy. Of those, 40 percent also harbor mutations in the PIK3CA gene, and are targeted by the PI3K-alpha inhibitor alpelisib (Novartis' Piqray). However, intrinsic and adaptive drug resistance is the norm with these agents and mechanisms of resistance are still largely unknown in the clinic.

In this webinar, Guotai Xu of Memorial Sloan Kettering Cancer Center will discuss results of CRISPR/Cas9 screens that he has run which suggest endocrine therapy and PI3K-alpha inhibitor resistance occurs  and may provide a basis to develop resistance therapeutic strategies to prevent or revert this resistance. Dr. Xu will share details of work in this area that was published in Nature in January 2020.

Sponsored by

Medical Geneticist, Genetic Laboratory,
Lyon University Hospital

This webinar will address the utility of exome sequencing for neurodevelopmental disorders research and will provide details of a comparison study of two exome probe kits in this field of study.

The genetic etiologies of many neurodevelopmental disorders, including epilepsy and intellectual disability, have been mapped out, and custom panels are available to help in their identification. Existing panels, while sufficient in detecting all variant classes, can be challenging for streamlining the lab workflow and for keeping up with frequent content updates. 

In this webinar, Dr. Gaëtan Lesca of Lyon University Hospital will share the results of a comparison of Roche’s SeqCap EZ MedExome Probes with the company’s new KAPA HyperExome Probes in a range of patients with neurodevelopmental disorders.

Attendees of this webinar will:

  • Gain a better understanding of the genetic etiologies of neurodevelopmental disorders
  • Appreciate the limitations of current tools to evaluate neurodevelopmental disorders
  • Understand the differences between the performance of the KAPA HyperExome Probes and Roche’s previous whole-exome sequencing solution.

For research use only. Not for use in diagnostic purposes.

KAPA, HYPEREXOME, and SEQCAP are trademarks of Roche. All other product names and trademarks are the property of their respective owner.

Sponsored by

Scientist II,
Ultragenyx Pharmaceutical

This webinar will discuss the use of digital spatial profiling to test a gene therapy for CDKL5 deficiency disorder (CDD), a rare X-linked neurodevelopmental disease that causes severe seizures, global developmental delay, and limits a patient’s ability to communicate.

Maggie Wright of Ultragenyx Pharmaceutical will outline her team’s approach to testing a gene therapy in a mouse model of CDD:

  • Adolescent CDKL5-/Y and CDKL5-/+ mice were administered the gene therapy AAV9-SYN-hCDKL5 via the intracerebral ventricular space
  • Distribution of the vector-derived hCDKL5 mRNA was assayed in the brain of these mice via RNAScope
  • Behavioral phenotypes of these treated mice were tested to determine efficacy of the treatment
Sponsored by

Director, Colorado Center for Personalized Medicine in the School of Medicine University

This webinar will provide an overview of how the Colorado Center for Personalized Medicine (CCPM) at the University of Colorado implemented a preemptive pharmacogenomic screening program via a large-scale research biobank and a robust biocomputing system.

CCPM is a multi-institutional collaboration to link extensive patient data to ‘omics’ information and promote development of optimal prognostic and diagnostic tools for the clinical setting.

The CCPM Biobank is collecting DNA from upwards of 500,000 consenting participants under a CLIA/CAP-compliant model. To date, more than 145,000 patients receiving care in the University of Colorado’s health system have consented to participate, and genetic data generated from Illumina’s Multi-Ethnic Genotyping Array (MEGA) have already been generated on the first 30,000. Exome sequencing of 100,000 patients per year is now underway.

To integrate high-dimensionality data being generated on biospecimens with the data captured in CCPM’s data warehouse, a robust computing resource was established. With this infrastructure in place, CCPM developed a clinical pharmacogenomic initiative, which includes preemptive return of clinical results via CCPM’s research biobank, automated clinical decision support (CDS) tools, and development and implementation of proactive strategies to engage stakeholders.

Sponsored by

Head of the Gene Technology Division, School of Biotechnology,
KTH Royal Institute of Technology

Recent advances in spatially resolved transcriptomics have greatly expanded the knowledge of complex multicellular biological systems. The importance of spatial context to infer deeper biological meaning is unquestionable, but technological constraints have historically limited broad adoption for various applications.

The field has quickly expanded in recent years, and several new technologies have been developed that aim to combine gene expression data with spatial information. The vast array of methodologies displays fundamental differences in their approach to obtain this information and, thus, demonstrate method-specific advantages and shortcomings. Nevertheless, the field of spatially resolved transcriptomics is accelerating in technological advancement, and the many biological analyses made possible by this advancement are just beginning to be fully explored.

In this webinar sponsored by 10x Genomics, Dr. Joakim Lundeberg of the KTH Royal Institute of Technology will present: 

  • A historical timeline of spatial gene expression methods
  • The current landscape of spatial transcriptomic methods as well as their strengths and weaknesses
  • Applications of spatial transcriptomics in a broad spectrum of research areas, including oncology, immunology, and neuroscience 
  • Future developments in spatially resolved transcriptomics and where the field is heading
Sponsored by
Thu
Sep
10
1:00 pm2020
Sponsored by
Genecentric

Development of RNA-Based Predictive Response Signatures as Companion Diagnostics

GenomeWebinar

Founder and Executive Partner, Opus Three

Senior Vice President, Clinical & Corporate Development, GeneCentric Therapeutics

This webinar, Part 2 of the “Advances in RNA-based Biomarker Development for Precision Oncology” webinar series sponsored by GeneCentric Therapeutics, will focus on the development of RNA-based companion diagnostics for oncology.

The path to developing a companion diagnostic (CDx) is becoming increasingly complex as available technologies and therapeutic advancements outpace regulatory standards and procedures. RNA-based approaches require heightened awareness and vigilance in combination with a well-defined and robust bioinformatics process. This webinar will cover the processof developing RNA-based predictive response signatures for cancer therapeutics; clinical and therapeutic implications for this approach; and the regulatory requirements, tools, and milestones necessary for successful advancement of an RNA-based CDx.

Felix Frueh, founder of regulatory consultancy Opus Three, will provide a deep dive into the regulatory considerations of developing RNA-based companion diagnostics. He will contrast the development of companion diagnostics with non-companion diagnostics and will illustrate key differences using a series of examples. Particular emphasis will be paid to potential future RNA-based companion diagnostics and currently marketed RNA-based diagnostics.

Joel Eisner of GeneCentric Therapeutics will follow with a clinical and bioinformatics perspective on the development of RNA-based predictive response signatures as companion diagnostics. His presentation will touch on the development of prototype response signatures using in silico analysis of public datasets, the curation of retrospective clinical data to further develop prototype predictive response signatures, and other points.

Sponsored by
Thu
Sep
17
1:00 pm2020
Sponsored by
Thermo Fisher Scientific

Clinical Diagnosis of Developmental Disorders with Chromosomal Microarrays

GenomeWebinar

Senior Director, Cytogenetics Laboratory,
Greenwood Genetic Center

The prevalence of developmental disability among US children aged 3 to 17 years increased between 2009 and 2017, with as many as 1 in 6 children in the US reported to have a developmental disability diagnosis. Developmental delay/intellectual disability (DD/ID) is frequently accompanied with one or more congenital anomalies or dysmorphic features. 

Chromosomal microarrays (CMA) are an established technology that has demonstrated great sensitivity and specificity for detecting genome-wide copy number variants (CNVs) and now represents a robust technical platform for both medical genetics research and clinical services. The American Academy of Neurology, the American College of Medical Genetics, and the International Collaboration for Clinical Genomics recommend CMAs as the first-line test to aid in the diagnostic evaluation of intellectual disability.

CMA is replacing traditional karyotype and FISH as the first-line genetic test due to its greater sensitivity, higher resolution, genome-wide capability, and greater diagnostic yield. The CytoScan Dx Assay is the first FDA-cleared chromosomal microarray test to aid in the identification of the underlying genetic cause of developmental delay, intellectual disability, congenital anomalies, or dysmorphic features in children.

Join Barb Dupont from Greenwood Genetic Center to: 

  • Learn about the importance of CMA postnatal assessments for developmental delay, intellectual disability, congenital anomalies, or dysmorphic features
  • Discover the advantages of using a higher-resolution CMA solution when compared to conventional techniques such as karyotyping and FISH
  • Understand how CMA results from CytoScan Dx Assay can be used in conjunction with other clinical and diagnostic findings by healthcare professionals
Sponsored by

Senior Research Associate,
Lawrence Berkeley National Laboratory

This webinar will discuss a streamlined library preparation method for next-generation sequencing (NGS) that improves quality control testing capability while reducing the total number of steps compared to conventional multiplexed library workflows.

NGS library preparation methods typically entail quality control testing at the end of the workflow, which can be laborious, particularly for high-throughput applications. The streamlined modification discussed in this webinar, Fluorescent Amplification for Next Generation Sequencing (FA-NGS), replaces PCR with real-time qPCR and SYBR Green to save time and implement single tube and single reagent QC.

FA-NGS enables in situ monitoring of library amplification and replaces the need for a separate quantification step of individual libraries. Additionally, FA-NGS allows for melting curve analysis as an intermediate library quality control step to aid in troubleshooting library failures prior to sequencing.

Attendees of this webinar will learn:

  • How to integrate qPCR and melting curve analysis into high-throughput NGS library preparation
  • Potential applications to various library workflows
Sponsored by

Chief Medical Officer, Basilea Pharmaceutica International

President and CEO, GeneCentric Therapeutics

This webinar, Part 3 of the “Advances in RNA-based Biomarker Development for Precision Oncology” webinar series sponsored by GeneCentric Therapeutics, will discuss novel and emerging applications of RNA-based genomic analysis in precision oncology, form characterizing the tumor microenvironment to informing the development of immuno-oncology treatments.

Marc Engelhardt of Basilea Pharmaceutica International will discuss work showing that differential induction of gene expression may explain differences in reported adverse event profiles of targeted anticancer agents. His talk will detail the analysis of gene expression induction in safety relevant normal tissues from patient-derived xenograft models as an approach to rationalize and identify the molecular basis of adverse event profiles of targeted anticancer agents.

Michael Milburn, President and CEO of GeneCentric, will follow with a discussion of the utility of bulk tumor RNA-seq analysis in drug development. In particular, he will cover aspects of specimen and study design for bulk tumor genomics, as well as advantages and challenges of RNA-based diagnostics over DNA variations.  Development of immunogenomic analyses and GeneCentric’s overall technology approach will be highlighted.  This includes looking beyond RNA transcriptomics and utilizing RNA sequence data in drug development.

Sponsored by

As cases of COVID-19 continued to grow this spring and summer in the US, so too did the number of Emergency Use Authorizations from the FDA for clinical diagnostic tests aimed at detecting current and past infections. The agency's policies for granting EUAs for both molecular and antibody tests evolved over time as more was learned about SARS-CoV-2 and its spread, and diagnostics firms and labs needed to adapt to these changes.

Dr. Elizabeth Hillebrenner, associate director for scientific and regulatory programs at the FDA's Center for Devices and Radiological Health, will kick off this virtual roundtable with an overview of the EUA program, how it evolved, and how lessons learned during the current pandemic may shape future policies and actions by the FDA. She will then take part in a panel discussion that will include a variety of stakeholders from the diagnostics and clinical lab industries. Panelists will include Dr. Robert Boorstein, Medical Director of Lenco Diagnostic Laboratories; Danelle Miller, VP, Global Regulatory Policy and Intelligence for Roche Diagnostics; Dr. Jeffrey Klausner, Professor of Medicine and Public Health at UCLA David Geffen School of Medicine and Fielding School of Public Health; and Gail Javitt, Director at Hyman, Phelps & McNamara.

Sponsored by
Recent GenomeWebinars
Thu
Aug
13
1:00 pm2020
Sponsored by
10x Genomics

Single-Cell and Spatial Transcriptomic Profiling of the Septic Kidney

GenomeWebinar

Assistant Professor of Medicine,
Indiana University School of Medicine

This webinar will discuss a study that combined single-cell gene expression and spatial gene expression to understand the evolution of sepsis in the kidney at the cellular and molecular level.

Understanding the pathophysiology of acute kidney injury is crucial for the comprehensive treatment of sepsis and its complications, but the exact cellular and molecular contributors to this multifaceted response remain unknown. Furthermore, the kidney is a highly complex organ, in which epithelial, endothelial, immune, and stromal cells are at constant interplay.  

In this webinar, Dr. Takashi Hato of Indiana University will describe a project that used both Chromium single-cell gene expression and Visium spatial gene expression solutions to provide a detailed and precise view of the evolution of sepsis in the kidney, as well as identify potential SARS-CoV-2 entry points.

Dr. Takashi Hato will discuss details of the study and its findings, including:

  • Comprehensive spatial and temporal transcriptomic profiling of the kidney in a murine sepsis model, extending from early injury well into the recovery phase 
  • Identification and localization of known and novel renal cell populations in the kidney microenvironment, including regional expression of essential components of the SARS-CoV-2 entry mechanism
  • Key changes identified in gene expression that altered cellular functions and explain features of clinical sepsis
  • How this rigorous spatial and temporal definition of murine sepsis will uncover precise biomarkers and targets that can help stage and treat human sepsis
Sponsored by