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GenomeWebinars: Recent

Jul
18
2024

Sponsored by Hologic

The Importance of Flexibility in Respiratory Testing Platforms: Accommodating Diverse Patient Needs and Changing Viral Incidence Throughout the Year

Respiratory testing decisions can be impacted by patient type (immunocompromised, pediatric, pregnant, elderly), patient risk (inpatient, outpatient, travel history, geography), and time of year (incidence of different respiratory viruses throughout the year). These unique attributes necessitate flexible testing algorithms to best serve varied patient populations and changing respiratory testing needs throughout the year. Additionally, streamlined workflows for respiratory testing can potentially decrease costs, hands-on time, and FTEs needed to process all samples in the laboratory.

In this webinar:

  • Rangaraj Selvarangan, director of the microbiology laboratory at Children's Mercy Hospital, will present clinical trial data on a recently FDA-cleared molecular test for respiratory viruses that detects and differentiates SARS-CoV-2, influenza A, influenza B, and RSV.
  • Jim Dunn, director of the medical microbiology and virology laboratories at Texas Children's Hospital, will review the respiratory testing algorithm used at the hospital, discussing how test ordering is modified throughout the year to accommodate seasonality, how different platforms are utilized to best serve patients, and how flexible testing platforms allow for optimal management of diagnostic stewardship.
  • Matthew Binnicker, medical director of the clinical virology laboratory at Mayo Clinic, will discuss the respiratory testing algorithm employed by a large reference laboratory with a diverse patient population, including a result masking strategy to accommodate different test order combinations. He will also review the 2023-2024 winter respiratory season experienced at Mayo Clinic and provide his perspective on what respiratory viral activity we might see in the year ahead.

Sponsored by

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Jul
11
2024

Sponsored by Roche

The Next Frontier: Key Considerations for Molecular Point-of-Care Testing for Sexually Transmitted Infections

Molecular testing for use at home and the point of care has boomed in the wake of the COVID-19 pandemic, and sexually transmitted infections have been a key area of focus for test developers and manufacturers after respiratory testing. Companies large and small have emphasized the importance of molecular point-of-care STI testing, particularly in light of rising rates of sexually transmitted infections in the US.

Now that molecular point-of-care testing technology has continued to advance, what are test users looking for in their tests and platforms, particularly when it comes to turnaround time or multiplexing? Where should test developers focus their efforts? How does molecular testing at both the point-of-care and at home fit in with other options for testing? What changes are on the horizon in the next three years as technology continues to develop?

In this virtual roundtable, our panel of experts on sexually transmitted infections and molecular point-of-care testing will discuss these questions. Our expert panelists include Jeffrey Klausner a clinical professor of medicine in infectious diseases at the University of Southern California; Thomas Schaus, head of R&D and scientific cofounder at molecular diagnostic company 3EO Health; Barbara Van Der Pol, professor of medicine and public health at the University of Alabama at Birmingham and director of the UAB STD Diagnostics Laboratory; and Yukari Manabe, professor of medicine and director of the Center for Innovative Diagnostics for Infectious Diseases at Johns Hopkins University.

Sponsored by

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Jul
11
2024

Sponsored by Sophia Genetics

Advancing Precision Oncology with a Matched Tumor-Normal Approach: Insights from the Clinic

This webinar presents an in-depth look at how Memorial Sloan Kettering Cancer Center (MSK) is routinely using its molecular assays — MSK-IMPACT and MSK-ACCESS — together to inform precision oncology approaches.

MSK-IMPACT is a targeted tissue-based sequencing test for comprehensive genomic profiling. MSK-ACCESS is a liquid biopsy test that enables non-invasive profiling and longitudinal disease monitoring. Together, they provide robust insights that help guide treatment decisions for improved outcomes in patients with advanced cancer. Unlike most tests, MSK leverages matched tumor-normal sequencing to remove germline and clonal hematopoietic variants, revealing genomic alterations of true somatic origin.

In this webinar, A. Rose Brannon, director of clinical bioinformatics at MSK, and Anita S. Bowman, associate director of clinical bioinformatics at MSK, will:

  • Highlight the benefits of matched tumor-normal sequencing to reduce biological false positives.
  • Discuss the clinical utility of combining tissue- and cell-free DNA-based sequencing approaches, with insights from real clinical cases.
  • Explore opportunities for clinical, translational, and basic research.

Sponsored by

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Jun
27
2024

Sponsored by SPT Labtech

Driving Throughput in tRNA Sequencing Library Generation With Automated Liquid Handling

Transfer RNAs (tRNAs) are critical adaptor molecules that translate genetic information into functional protein sequences, dictating the fidelity of translation processes in the cell. High-resolution sequencing-based methods for tRNA sequencing have provided transformative insights into the physiological impact of tRNA expression, modification, and aminoacylation (charging) levels on cellular stress and disease conditions. Additionally, large-scale genome engineering efforts have employed tRNA sequencing to recapitulate the translational state of engineered cells. However, tRNA sequencing has not been widely adopted due to the time-consuming, arduous, and specialized nature of library generation workflows.

In this webinar, Russel Vincent of the Church Lab and Biopolymers Genomics Core Facility (BPF) at Harvard Medical School will describe how he and colleagues streamlined library generation for tRNA sequencing using SPT Labtech’s Firefly all-in-one automated liquid handling platform. This method delivers significant time savings in the lab by reducing a previously multi-day workflow to a single day, while improving throughput and reducing experimental variation.

The speakers will present:

  • An introduction to automated tRNA Sequencing: Hear first-hand experience of automation-enabled tRNA sequencing technology.
  • How the versatility of the Firefly liquid handling platform enables the development of reliable and modular library preparation protocols for NGS.
  • Sequencing applications, such as genome engineering, genetic code expansion, and investigating cellular stress.

Sponsored by

SPT Labtech
Jun
26
2024

Sponsored by Complete Genomics

Revolutionizing Personalized Medicine Through Metagenomic Sequencing Strategies

In the quest to unlock the potential of personalized medicine, metagenomic sequencing emerges as a powerful tool. By analyzing the collective genetic material of microbial communities inhabiting the human body, metagenomics offers insights into individual health and disease. From understanding the microbiome’s role in various physiological processes to identifying microbial signatures associated with specific conditions, metagenomic sequencing provides a comprehensive view of an individual’s health status. Furthermore, the integration of metagenomic data with clinical information enables tailored therapeutic interventions, paving the way for precision healthcare.

In this webinar, Maike Seifert of the Center for Translational Microbiome Research/ National Pandemic Center at the Karolinska Institute will explore the latest advancements in metagenomic sequencing technologies and their implications for personalized medicine, emphasizing the promising opportunities and challenges ahead.

Sponsored by

Complete Genomics
Jun
25
2024

Sponsored by Roche

Unlocking the Power of CGP: Considerations for Implementing a High-Quality In-House Workflow

Increased adoption of personalized medicine has brought comprehensive genomic profiling (CGP) to the forefront of cancer research. Ideally, a CGP assay for FFPE tissue maximizes insights from limited biopsy samples and is straightforward to implement and operate in the laboratory. There are many considerations for building an in-house CGP solution, such as staffing, turnaround times, quality control, changing technologies, and the discovery of new alterations. Assay-specific differences, including workflow, bioinformatics, reporting, and the complex interplay of these elements, are important challenges for implementing and achieving uniformity in CGP testing.

In this webinar, Eric Thompson and Thomas Wieland* will discuss their work evaluating the implementation of an in-house CGP kit as well as the performance of the Avenio Tumor Tissue CGP Kit (RUO). The kit was found to have high intra- and inter-lab reproducibility and a high degree of alignment with FoundationOne CDx. The kit was also compared, in combination with Navify Mutation Profiler (RUO) tertiary analysis software, to the TruSight Oncology 500 RUO assay paired with PierianDx Clinical Genomics Workspace software.

The speakers will discuss:

  • The importance of CGP in cancer research.
  • Benefits of bringing CGP in house.
  • Factors to consider when implementing an in-house workflow, with a special focus on the quality of results.
  • Study data for the CGP kit on:
    • Alignment with FoundationOne CDx.
    • Reproducibility within and between labs.
    • Performance as compared with TSO 500.
  • Secondary analysis and bioinformatics complexities and relevance.
  • The new Avenio Tumor Tissue CGP Kit V2.

*Foundation Medicine is owned by the webinar sponsor, Roche.

Sponsored by

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Jun
20
2024

Sponsored by Thermo Fisher Scientific

Sequencing IGH Chains for Somatic Hypermutation Analysis and Immuno-Oncology Translational Research

Next-generation sequencing of rearranged IGH chains (BCR-seq) provides exceptional resolution of the human B-cell repertoire and is now an established tool for clinical research and immunology translational research.

In this webinar, Timothy Looney will describe the advantages of BCR-seq as a tool for determining the somatic hypermutation status of chronic lymphocytic leukemia (CLL) and highlight emerging translational research applications of BCR-seq as a biomarker discovery tool for adenosine pathway inhibition immunotherapy.

Learning objectives:

  • Understand how next-generation sequencing of rearranged IGH chains (BCR-seq) may be used to assess the status of the human B-cell repertoire.
  • Describe the advantages of BCR-seq as a tool for determining the somatic hypermutation status of CLL.
  • Highlight emerging translational research applications of BCR-seq as a biomarker discovery tool for adenosine pathway inhibition immunotherapy.

Sponsored by

Jun
18
2024

Sponsored by Velsera

Alterations in the Tumor Microenvironment and Key Signaling Pathways in Canine Gliomas Mirror Those Seen in Human Patients

Malignant gliomas are the most common type of primary brain tumors, with patient outcomes that are generally dismal. Gliomas in pet dogs occur at similar rates to those seen in humans, and recently, pet dogs have been assessed as a valuable model in which to study gliomas.

In this webinar, Nadia Lanman, a research associate professor in the Department of Comparative Pathobiology at Purdue University, will discuss work in which she and colleagues compared naturally occurring canine and human gliomas, focusing on the tumor microenvironment (TME) and key pathways dysregulated in human gliomas.

The team found that key canonical pathways that are altered in human gliomas are also altered in canine gliomas. A comparison of high-grade gliomas in pet dogs to normal canine brain tissues showed significant abnormal gene expression in three canonical oncogenic pathways of human glioblastoma multiforme. Similarities between species included increased expression of PDGF, and receptors PDGFRA and PDGFRB. Frequent copy number alterations and mutations were also observed in PDGFRA and EGFR. Differences between species include the mutation rate of TP53 and IDH1 expression. Although an analysis of the TME from RNA-seq data revealed an influx of immune cells in adult, pediatric, and canine gliomas, there was a concurrent influx of immunosuppressive cells.

Sponsored by

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Jun
13
2024

Sponsored by Foundation Medicine

Incorporating Biomarkers in Early- and Late-Stage Clinical Trials

Clinical trials are often the longest and most challenging part of the winding journey from drug discovery to commercialization. Precision medicine and biomarkers have created the opportunity to move faster and increase the chances of success, with studies showing that trials using biomarkers have two to six times the overall probability of success compared to trials without biomarkers. However, many options exist, and questions remain about how to best incorporate biomarkers and how to make tradeoff decisions at different stages of clinical research and trial development. Which biomarkers are best for Phase Ib versus Phase II? How should drug development programs think about incorporating ctDNA monitoring? What is the latest FDA thinking on trial design? How are requirements different for enrollment in different global markets?

In this webinar, Abdul Rafeh Naqash will offer answers to questions like these and provide examples of the value and considerations that drug developers should be thinking about when incorporating biomarkers in different phases of clinical trials. He will highlight evidence for specific biomarkers like ctDNA, describe the different opportunities for tissue- or blood-based enrollment depending on the cancer indication or patient population, and offer insights from his experience as a researcher and medical oncologist.

David Fabrizio, vice president of partner innovation at Foundation Medicine, will present data on Foundation Medicine's portfolio for Phase I, Phase II, and Phase III clinical trials and discuss exciting new opportunities for researchers and drug developers to add value and gain insights at each phase of their clinical programs.

Sponsored by

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Jun
11
2024

Sponsored by Pillar Biosciences

Streamlining the Clinical Laboratory Workflow of Myeloproliferative Neoplasms With Next-Generation Sequencing

The standard of care for evaluating myeloproliferative neoplasms (MPN) involves the molecular analysis of three driver genes: JAK2, CALR, and MPL. Typically, individual single-gene tests are performed sequentially following a standard clinical reflex cascade algorithm to identify alterations associated with polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF).

Currently, common diagnostic workflows involving reflex PCR provide inadequate turnaround time, may potentially introduce errors, and can be expensive to manage due to reagents and/or technologist time. To be more efficient, minimize laboratory costs, and reduce turnaround time, NGS can be utilized as a new tool to evaluate these three driver genes at one time and provide clinically actionable, qualitative, or quantitative results. 

Learning Objectives

  • Review challenges associated with the current laboratory standard of care for the clinical evaluation of myeloproliferative neoplasms.
  • Discuss the evaluation, validation, and workflow assessment of an NGS-based workflow to help evaluate and classify MPN.
  • Examine the clinical and financial impact associated with this new  NGS-based workflow.

Sponsored by

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Jun
06
2024

Sponsored by Hologic

Tick Talk: Developing and Implementing High-Throughput Vector-Borne Disease PCR Testing for Clinical and Surveillance Applications

With milder winters and warmer summers, the range of tick species and the diseases they carry continue to expand in the US. The pathogens that cause these diseases are conventionally detected with manual, labor-intensive PCR testing methods. As detected cases of various tick-borne pathogens continue to increase and staffing constraints impact testing facilities across the diagnostic laboratory landscape, there is an urgent need for high-throughput, fully automated testing solutions.

In this webinar, two speakers will discuss their development and implementation of high-throughput, fully automated PCR laboratory-developed tests using Hologic’s Open Access functionality on the Panther Fusion system to support clinical and environmental surveillance efforts in their regions.

Kathleen Stellrecht, director of molecular diagnostics, pathology, and laboratory medicine at Albany Medical Center will speak to her lab’s successful development and implementation of lab-developed tests to address rising cases of anaplasmosis, ehrlichiosis, and babesiosis, providing a more streamlined laboratory workflow and positively impacting patient healthcare outcomes.

Megan Ahmann, an infectious disease fellow with the Association of Public Health Laboratories, who currently supports Iowa State Hygienic Laboratory, will discuss the development and implementation of a PCR lab-developed test to detect Rickettsia species, sampling pooled ticks to streamline environmental surveillance efforts.

During this webinar, presenters will discuss:

  • Impact of implementing high throughput RT-PCR testing to address increased testing volumes for vector-borne pathogens.
  • Assay development and workflow optimization strategies for expanded PCR testing using the Open Access functionality on Panther Fusion.
  • Evolving distribution of tick species in certain regions of the US.

Sponsored by

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Jun
05
2024

Sponsored by Thermo Fisher Scientific

Unraveling the Roles of Copy Number Variants in Tumorigenesis

Genomic analysis of cancer cells has revealed comprehensive mechanisms of tumorigenesis in human patients. Among the abnormalities discovered so far, copy-number variants (CNVs) account for a significant portion of the frequently observed pathogenic variants and serve as important biomarkers for early detection and follow-up.

OncoScan CNV assays are widely used as CNV analysis tools for solid tumor samples, display robust ability in detecting LOH and the CNVs that play an essential role in cancer origination, progression, and metastasis. The assays have the advantage of processing highly degraded and/or low-quality samples, which is frequently observed in solid tumor samples.

In this webinar, Xiaolan Fang, associate director of the cytogenomics and molecular pathology laboratories of the Henry Ford Health System, will discuss the development and application of OncoScan CNV assays in a research setting to decipher molecular and cytogenetic mechanisms in a few representative types of solid tumors.

Attendees will:

  1. Explore the evolution and development of cytogenetics and cytogenomics throughout history.
  2. Gain familiarity with the current tools and techniques used in cytogenetic analysis.
  3. Understand the unique advantages and benefits of OncoScan in comparison to other array/NGS platforms for cytogenomic analysis.
  4. Gain knowledge about the specific types of tumor samples that can be effectively analyzed using OncoScan technology.

Sponsored by

May
30
2024

Sponsored by SomaLogic

Predictive Modeling and Reliable Biomarker Discovery in Clinical Omics Studies

High-content omics technologies coupled with machine-learning methods have transformed the biomarker discovery process. However, the translation of computational results into scalable clinical biomarkers remains challenging. A rate-limiting step is the rigorous selection of reliable biomarker candidates among a host of biological features.

In this webinar, drawing examples from real-world clinical omics studies, Julien Hédou will introduce Stabl, a general machine-learning framework that identifies a sparse, reliable set of biomarkers by integrating noise injection and a data-driven signal-to-noise threshold into multivariable predictive modeling.

Sponsored by

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May
16
2024

Navigating the Complexities and Controversies of Integrative Molecular Strategies in Oncology

This webinar is part two of the two-part Precision Oncology News Virtual Molecular Tumor Board series.

The advent of precision oncology has transformed the therapeutic landscape for patients, presenting a paradigm shift from one-size-fits-all approaches to individualized treatment strategies. 

This presentation will recognize the intricate balance between the potential of various assays to guide treatment decisions and the controversies surrounding their interpretation and clinical utility. Our panelists will highlight the critical importance of Variant Allele Frequency (VAF) as a biomarker for tumor burden and treatment response, as well as explore the burgeoning field of Molecular Residual Disease (MRD) assays with a focused lens on their application in solid tumors. In addition, the concurrent application of tissue-based and liquid-based Next-Generation Sequencing (NGS) testing represents a cornerstone in the evolution of diagnostic modalities. By weaving together the threads of sequencing, VAF, and MRD assays, our presentation aims to feature the synergy of these technologies in advancing precision oncology, while acknowledging the challenges and debates that shape this dynamic field.

May
16
2024

Sponsored by Oxford Nanopore Technologies

Advancements in Nanopore Sequencing for Enhanced Food Safety and Quality Assurance

Food safety and quality assurance are paramount concerns in the food industry, necessitating continual innovation in testing methodologies. In July 2020, the FDA introduced a New Era of Smarter Food Safety blueprint that outlines a partnership between government, industry, and public health advocates based on a commitment to further modernize food safety.

This webinar will delve into the impact of real-time nanopore sequencing on food safety — including quality assurance — within the public and private sectors. Food microbiologists will share how new genomic tools can help create a safer and more digital, traceable food system, as outlined in the FDA’s blueprint for a New Era of Smarter Food Safety.

Cameron Parsons, an R&D scientist at Mérieux NutriSciences, will explore how long-read sequencing can help provide a deeper understanding of the microbial diversity in food products, differentiate multiple pathogens within the same complex food sample, and identify the foodborne pathogen Salmonella more definitively.

Marc Allard, a research microbiologist at the FDA Center for Food Safety and Applied Nutrition, will discuss the achievements of the GenomeTrakr network, a coalition of laboratories sharing whole-genome data for source tracking foodborne pathogens. He will also discuss the benefits of the network’s open data model, which allows greater transparency between federal/state agencies and industry, academic, and international collaborators.

Sponsored by

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