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GenomeWebinars: Recent

Oct
21
2021

Sponsored by Beckman Coulter Life Sciences

Achieving Cell-Free Gene Expression with Acoustic Liquid Handler

This webinar is part one of a two-part series on abstract cell-free expression.

The current generation of cell-free expression systems is used for a wide variety of applications, ranging from research to artificial cell design. However, before a successful design of these applications is made, many rounds of prototyping need to be performed. In this webinar, we discuss how Echo Acoustic Liquid Handlers (LHs) from Beckman Coulter Life Sciences have become invaluable equipment for testing cell-free systems, regulatory components, and genetic circuits by accelerating the process of prototyping five to 10 times faster than performing experiments by hand.

This presentation covers:

  • Overview of cell-free transcription and translation (TXTL) and its applications
  • Overview and specifications of Echo LHs
  • The advantages of using Echo LHs in a cell-free synthetic biology lab
  • Examples of applying the Echo 525 and Echo 650 LHs in the lab

Sponsored by

Oct
20
2021

Sponsored by Lexogen

A Multidisciplinary Study Links Androgen Signaling with Severe COVID-19 Symptoms in Men

This webinar will discuss a study that identified a link between male sex hormones and COVID-19 disease severity in men and also pointed toward possible therapeutic candidates for the disease.

Dr. Hani Goodarzi of the University of California, San Francisco, will share details of the work, which was based on the premise that SARS-CoV-2 infection occurs through binding of the viral spike protein to angiotensin converting enzyme 2 (ACE2) on the host cell membrane.

Dr. Goodarzi and colleagues used a high-throughput drug screening strategy to identify therapeutic candidates that reduce ACE2 levels in cardiac cells derived from human embryonic stem cells (hESCs). Analysis of validated hit compounds pointed to the central role of androgen signaling in ACE2 expression.

Treatment with antiandrogenic drugs, as well as in silico-derived compounds predicted to target this pathway, reduced ACE2 expression and protected hESC-derived lung organoids against SARS-CoV-2 infection.

Finally, clinical data on COVID-19 patients demonstrated that prostate diseases, which are linked to elevated androgen, are significant risk factors for severe COVID-19 and that genetic variants that increase androgen levels are associated with higher disease severity.

Dr. Goodarzi will discuss how these findings offer insights on the basis of differential susceptibility between men and women and suggest antiandrogenic drugs as candidate therapeutics for COVID-19.

Sponsored by

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Oct
19
2021

Sponsored by Cepheid

The Importance of Rapid, Accurate, and Reproducible Molecular Results for CML Monitoring

In 2018, there were an estimated 61,698 people with chronic myeloid leukemia (CML) in the United States, according to the National Institutes of Health. Even though advances in treatment and care have transformed CML into a manageable disease, several significant challenges remain in monitoring therapeutic response and disease progression.  

Please join us on October 19th to discuss CML and the importance of accurate and fast monitoring with two speakers, Dr. Bijal Parikh and Dr. Yitz Goldstein. Dr. Parikh is the Medical Director of the Barnes-Jewish Hospital Molecular Diagnostics Laboratory and Associate Medical Director of the Molecular Infectious Disease and HLA Laboratories. Dr. Goldstein is the Director of the Genomic Laboratories at Montefiore Medical Center and the Director of Clinical Virology. 

The discussion will touch on the revolution of Tyrosine kinase inhibitors and their resistance, the current CML guidelines, and the clinical impact of different assays. Additionally, our speakers will provide a first-hand perspective on the clinical value of rapid molecular CML monitoring and its effect on patient care. 

Sponsored by

Oct
18
2021

Sponsored by Thermo Fisher Scientific

Institutional Lessons From Implementing Plasma Genotyping to Monitor Response and Treatment in Non-Small Cell Lung Cancer

Nearly 70 years after the discovery of cell-free DNA, plasma genotyping is routinely used to non-invasively detect and quantify clinically relevant point mutations, insertions/deletions, amplifications, rearrangements, and aneuploidy. Over the past eight-plus years, strong concordance has been shown between plasma and tissue-based genomic assays, encouraging the clinical adaptation of plasma genotyping. In this webinar, Dr. Cloud Paweletz will present institutional experiences implementing liquid biopsies into non-small cell lung cancer. He will discuss technical limitations and lessons learned with a particular focus on minimal residual disease, treatment response, and the emergence of resistance monitoring. The realization of these lessons, however, spurs significant investment in techniques and technologies to increase specificity and sensitivity and reduce turnaround time and cost for further clinical adoption of this promising diagnostic.

Sponsored by

Oct
15
2021

Sponsored by Cepheid

Antimicrobial Resistance in the Wake of COVID-19: How Healthcare Systems Can Use Molecular Testing to Stem the Tide

As the COVID-19 pandemic rages on, data have shown that other aspects of healthcare are being neglected by patients and physicians alike, including practicing good stewardship to battle antibiotic-resistant bacteria. Earlier this year, the US Centers for Disease Control noted that COVID-19 can create a "perfect storm" for antibiotic-resistant infections in healthcare settings due to longer hospital stays, staffing shortages, a higher number of sick patients, and difficulties implementing infection control practices. The CDC also noted that the number of bacterial and fungal specimens and isolates received and/or tested in 2020 by CDC's antibiotic resistance lab network was about 23 percent less than 2019 levels.

More recently, in September, a CDC study published in Infection Control and Hospital Epidemiology revealed initial increases early in 2020 for ventilator-associated events (VAEs), central line-associated bloodstream infections (CLABSIs), and methicillin-resistant Staphylococcus aureus (MRSA) bacteremia. In addition, compared to 2019, the second half of 2020 saw large and significant increases in catheter-associated urinary tract infections, VAEs, CLABSIs, and MRSA bacteremia.

Although it is still unclear whether this is a burgeoning trend or a blip on the radar, molecular testing remains one of the most important public health tools available for keeping antibiotic resistance in check. In this roundtable discussion, researchers and lab directors from four highly renowned US academic institutions and healthcare organizations will share their thoughts on what they're seeing on the antimicrobial stewardship front; the role of molecular testing in combatting AMR; what challenges they are seeing in their organizations; and what tools and technologies are available or on the horizon to help with the fight.

The session will include a live Q&A in which attendees can post questions to our panelists: Kevin Alby, Ph.D., D(ABMM) (Assistant Professor, Pathology and Laboratory Medicine Director, Bacteriology and Susceptibility Testing, Associate Director, Clinical Microbiology Laboratory, UNC School of Medicine, Chapel Hill, NC); Romney M. Humphries, Ph.D., D(ABMM), M(ASCP) (Professor of Pathology, Microbiology, and Immunology Medical Director of the Microbiology Laboratory); Dr. Patricia Simner, PhD, D(ABMM) (Associate Professor of Pathology at the Johns Hopkins University School of Medicine, Director of the Medical Bacteriology and Infectious Disease Sequencing Laboratories at the Johns Hopkins Hospital); Glen Hansen, PhD (Hennepen Healthcare).

Sponsored by

Oct
14
2021

Sponsored by BD

Multiomic Analysis of Immune Regulation in Triple-Negative Breast Cancer Points to New Therapeutic Strategies

Checkpoint inhibitors have revolutionized cancer treatment, but only a small proportion of breast cancer patients have shown benefit from immunotherapy. One of the factors limiting the effect of immunotherapies is the presence of tumor-educated immunosuppressive myeloid populations that inhibit anti-cancer T-cell cytotoxic killing activity.

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous and poorly defined group of tumor-infiltrating myeloid progenitors that contribute to cancer progression and metastasis. MDSCs are a compelling target for cancer therapy, but their high heterogeneity and poor definition hamper the development of anti-cancer MDSC-based therapy.

In this webinar, David Gallego Ortega of the University of Technology Sydney School of Biomedical Engineering will discuss a study that used single-cell RNA-seq in mouse models of triple-negative breast cancer (TNBC) to create a spatiotemporal atlas of inflammation associated with metastatic breast cancer cell dissemination. This high-resolution map of the cellular composition and functional diversity of inflammatory cells identified a subclass of granulocytic MDSCs involved in the formation of the pro-metastatic niche and progression to metastatic disease.

Dr. Ortega’s team further characterized this pro-metastatic MDSC subclass integrating a high-dimensional cell surface antibody panel (18 FACS antibodies + 91 AbSeq antibodies) to the single-cell whole-transcriptome profiling of MDSCs to uncover immunosuppressive pathways and molecular targets with potential therapeutic value.

This high-resolution multiomic definition of pro-metastatic MDSCs is a step forward for designing new strategies to efficiently reprogram immunosuppressive cell populations and stimulate antitumor immunity, ultimately paving the way for the development of the next generation of immunotherapy for aggressive breast cancer.

Learning objectives include:

  • Building a spatiotemporal atlas for deep characterisation of cell states during the pre-metastatic niche formation at the single-cell level
  • Integrating a high-dimensional cell surface antibody panel (18 FACS antibodies + 91 AbSeq antibodies) and single-cell whole-transcriptome profiles of protumorigenic MDSCs 
  • Designing new strategies to efficiently reprogram immunosuppressive cell populations and stimulate antitumor immunity

Sponsored by

Oct
13
2021

Sponsored by Akoya Biosciences

MITRE Study: Standardizing Spatial Phenotyping and Biomarker Analysis with Multiplexed Immunofluorescence in Immuno-Oncology

In this webinar, Dr. Bernard Fox and Elizabeth Engle will discuss the results of the Multi-Institutional TSA-amplified Multiplexed Immunofluorescence Reproducibility Evaluation (MITRE Study), published in the Journal for ImmunoTherapy of Cancer (JITC) in July 2021. The MITRE study is the first multi-institutional study involving multiplexed immunofluorescence (mIF) designed to develop and validate a spatial biology workflow that is transferable among sites and delivers site-independent and reliable quantitative data for immunotherapy research. The MITRE results are an important step toward standardizing an automated mIF-based spatial biology workflow that provides the level of performance needed to support clinical trials and that can be applied to clinical testing in the future.

In this talk, attendees will:

  • Review evidence that evaluating the immune landscape of cancer can inform a patient’s prognosis and provide predictive biomarkers for response to therapy. 
  • Learn about the MITRE study and the evidence it provides on the standardization of an automated spatial biology workflow for clinical and translational research.
  • Understand the value of spatial biomarkers and how they allow researchers to map the interactions of tumor and immune cells across an entire tumor tissue section without destroying the spatial context of the tissue, enabling a more accurate assessment of tumor-immune biology.
  • Learn how the Phenoptics mIF solution is being used by researchers to develop spatial biomarkers for trials and eventual clinical use.

Sponsored by

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Oct
12
2021

Sponsored by 10x Genomics

Spatial Genomics in the Era of Immunotherapy … and COVID-19

This webinar will discuss the applications of spatial transcriptomics for elucidating the molecular mechanisms of immunotherapy response as well as the pathogenesis of SARS-CoV-2.

Arutha Kulasinghe, Spatial Biology Group Leader at the University of Queensland, will discuss recent advances in the use of spatial transcriptomics, which provides unprecedented insights into tissue architecture and cellular activation status.

Dr. Kulasinghe will provide an overview of spatial genomics and proteomics as well as the landscape of current technologies and applications in basic and clinical research. He will also discuss two recent studies from his team: one that applied spatial transcriptomics to identify predictive biomarkers for immunotherapy and another that used spatial transcriptomics to identify host response signatures in patients infected with SARS-CoV-2. These studies highlight the use of spatial transcriptomics for biomarker discovery approaches.

Dr. Kulasinghe will also address future directions and applications for spatial biology in translational research and pathology.

Sponsored by

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Oct
12
2021

Sponsored by DNA Script

Custom Library Adaptors Via Enzymatic DNA Synthesis Improve Precision of Real-Time Nanopore Sequencing

This webinar will discuss how benchtop enzymatic DNA synthesis enables the rapid creation of oligonucleotides that can be combined with real-time nanopore DNA sequencing to accelerate iterative design and testing cycles in synthetic biology.

Tim Mercer of the Australian Institute of Bioengineering and Nanotechnology will share how his team uses enzymatic DNA synthesis to build novel, custom library adaptors, termed CAPTORS, that contain functional sequence elements that can measure the qualitative and quantitative accuracy of a DNA sequencing library. Dr. Mercer will demonstrate how CAPTORS are used to prepare libraries from patient samples, with the functional information retrieved during nanopore sequencing.

In one example of the applications for this work, Dr. Mercer will show how the analysis of CAPTORS using adaptive sequencing allows real-time evaluation of sequencing accuracy at per-read, per-pore, and time level during metagenome experiments in the Nevada Toluca volcano near Mexico City.

CAPTORS can also analyze quantitative accuracy, improving measurements of gene expression in mRNA samples, and enabling best-in-class normalization between samples across large patient cohorts, longitudinal patient timelines, and point-of-care testing. These benefits can also be employed to improve clinical diagnosis, with CAPTORS able to sufficiently mitigate nanopore sequencing errors to improve the diagnosis of pathogenic BRCA1/2 variants in breast cancer.

Together, this demonstrates how the enzymatic synthesis of CAPTORs can affix information within patient samples during library preparation that is later retrieved by sequencing. The information encoded within CAPTORS can act as internal ‘software’ that interfaces with external bioinformatic software for responsive analysis, and can integrate patient samples into a large decentralized global network or a clinical IT infrastructure.

Sponsored by

Oct
06
2021

Sponsored by Akoya Biosciences

I-SPY 2 Trial Innovations: Clinical Trial Design and the Use of Spatial Biomarkers

The I-SPY 2 (investigation of serial studies to predict your therapeutic response with imaging and molecular analysis) is an adaptive clinical trial platform that supports the rapid, focused clinical development of paired oncologic therapies and biomarkers. The goal is to identify improved treatment regimens based on the molecular characteristics of individual patients’ disease.

In this webinar, Drs. Laura Esserman and Michael Campbell will discuss the I-SPY 2 trial of neoadjuvant treatment for locally advanced breast cancer. The trial involved the use of Multiplex Immunofluorescence (mIF) based biomarker panels, developed with the Akoya Phenoptics platform, to map the heterogeneity of the tumor microenvironment.

Drs. Esserman and Campbell have standardized biomarker discovery and development efforts on the Phenoptics platform to measure as many as six markers at a time on a single pathology slide using multiplex immunofluorescence.  They will discuss how I-SPY 2 has the potential to significantly accelerate the time to get effective treatments to the patients who will benefit, while also reducing the cost of drug development.

In this talk, attendees will:

  • Learn how the I-SPY 2 trial’s innovative adaptive trial design has accelerated the pace of new drug development in oncology through improved clinical trials and biomarker use for breast cancer.
  • Understand the value of spatial biomarkers and their use in the I-SPY trials to serve as predictors of response to immuno-oncology drug combinations.
  • Learn how fundamental innovations deriving from the I-SPY 2 trial are improving clinical trials and patient care on many levels and how a number of these advances have become best practices.

Sponsored by

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Oct
05
2021

Sponsored by Natera

Advances in ctDNA-Guided Treatment Decisions in Urothelial Carcinoma

The recent publication of IMvigor010 trial data demonstrates the strength of circulating tumor DNA (ctDNA) testing post-cystectomy in muscle-invasive bladder cancer (MIBC) to help identify patients likely to benefit from immunotherapy. The data analysis demonstrated both the prognostic and the predictive value of molecular residual disease (MRD) testing in this patient population. In this webinar, Thomas Powles, professor of genitourinary oncology and director of the Barts Cancer Centre, will share the findings of the IMvigor010 data analysis, present relevant MIBC publications, and discuss the IMvigor011 Phase III trial.

Join the discussion of this and other potential applications of ctDNA in urothelial carcinoma:

  • Surveillance monitoring with ctDNA could allow for earlier detection of relapse on a molecular level and potentially allow clinicians to treat patients at low levels of disease burden.
  • Treatment response monitoring of MRD could predict outcomes as early as week six into adjuvant therapy.
  • Post-TURBT treatment decisions for Stage I or lower patients could be enhanced by assessing MRD.
  • Further research of ctDNA testing in the neoadjuvant setting in bladder cancer could potentially create a pathway for Stage II and Stage III patients to avoid cystectomy.

Sponsored by

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Sep
30
2021

Sponsored by Agena Bioscience

The Promise of Liquid Biopsy for Individualizing Cancer Care

This webinar will provide an overview of how liquid biopsies – the molecular analysis of circulating cell-free tumor DNA (ctDNA) released into the blood - can provide new insights into tumor biology and help personalize patient care.

Klaus Pantel, Chairman of the Institute of Tumor Biology at University Medical Center Hamburg-Eppendorf, will discuss how liquid biopsy analyses can provide information for the early detection of cancer and identify cancer patients at risk of relapse. The approach may also serve to monitor tumor evolution, therapeutic targets, or mechanisms of resistance on metastatic cells.

Liquid biopsies show particular promise for metastatic cancers. Repeated needle biopsies of metastatic lesions are invasive and some locations are difficult to access. In contrast, monitoring of blood samples is only minimally invasive and can identify tumor evolution and tumor subtype switches, which may then lead to the selection of appropriate therapies based on the molecular composition of recurrent metastases.

Prof. Pantel will also discuss the importance of technical standardization and clinical validation of liquid biopsy assays.

Dr. Alexander Sartori from Agena Bioscience will follow with an overview of Agena’s MassArray System and available variant panels for circulating cell-free DNA in various cancers.

Sponsored by

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Sep
29
2021

Sponsored by Millipore Sigma

Development of New Metabolism-Based Multi-Cancer Biomarkers to Detect the Earliest Stages of Cancer

This webinar will address the need for innovation in the early detection of cancer and the approach taken by Elypta, a Swedish cancer detection firm, to develop new metabolism-based biomarkers.

Elypta was funded by the EU Horizon 2020 program to bring the first kidney cancer recurrence test to market. Elypta’s approach is based on profiling glycosaminoglycans — or the GAGome — and developing scores indicative of cancer. At the 2021 American Society of Clinical Oncology conference, a proof-of-concept study across 14 cancer types revealed the broader potential for early detection using the technology, highlighting the sensitivity to stage I disease.

Karl Bergman, CEO of Elypta, will discuss the need for new cancer biomarkers and Elypta’s results highlighting the potential of glycosaminoglycans as a tool in early detection. He will also outline the path Elypta took to develop their research-use-only (RUO) kits, partnering with MilliporeSigma at an early stage to ensure a clear path to large-scale in vitro diagnostic (IVD) manufacturing and enabling the Elypta team to focus their efforts on research and development.

Michael Mitchell, commercial project manager at MilliporeSigma, will discuss the milestones and challenges of MilliporeSigma’s work with Elypta. Mitchell will cover highlights from the set-up, pilot, and engineering phases of Elypta’s RUO cancer detection kit, as well as the preparative work for their IVD offering.

Attendees will learn:

  • Why more biomarkers are needed for the earliest stages of cancer
  • Key aspects and results from the GAGome-based liquid biopsy platform developed by Elypta
  • How a partnership with MilliporeSigma helped Elypta in the development journey

Sponsored by

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Sep
28
2021

Sponsored by BD

Single-Cell Proteogenomic Reference Maps of the Hematopoietic System Enable Massive Profiling of Precisely Defined Cell States

Single-cell genomics has transformed our understanding of complex cellular systems. However, excessive costs and a lack of strategies for the purification of newly identified cell types have impeded functional characterization and large-scale profiling.

In this webinar, Sergio Triana of the European Molecular Biology Laboratory and Dominik Vonficht of the German Cancer Research Center will describe their latest work, where they generated high-content single-cell proteogenomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia.

These reference maps enable cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems, and permit the purification of precisely defined cell states.

Triana and Vonficht will discuss how the systematic integration of cytometry and proteogenomic data enabled them to measure the functional capacities of precisely mapped cell states at the single-cell level.

Learning objectives:

  • Understand the experimental design needed to apply single-cell multiomics to healthy and diseased bone marrow
  • Learn how to use surface marker profiling to generate gating schemes to purify molecularly defined populations
  • Review different approaches to apply and validate new gating schemes on rare populations in the bone marrow

Sponsored by

Sep
23
2021

Sponsored by Ionpath

Next-Gen Multimodal Spatial Analytical Methods for Understanding Tissue Responses to Infection and Cancer

A thorough understanding of complex spatial host-disease interactions in situ is necessary to develop effective preventative measures and therapeutic strategies. Techniques that can take advantage of the high-resolution spatial tissue phenotyping capabilities of Multiplexed Ion Beam Imaging while providing a multiomic readout with robust data analysis tools are critical to this effort.

In this webinar, Sizun Jiang, Principal Investigator at Beth Israel Deaconess Medical Center, will discuss recent work on spatial methodologies and frameworks broadly applicable to deciphering tissue responses to various malignancies, including infectious diseases and tumor biology. These methodologies include:

  • Simultaneous measurements of protein and nucleic acids in tissues with Protein And Nucleic acid IN situ Imaging (PANINI)
  • Robust correction for lateral spillage of cell surface markers between adjacent cells using REinforcement Dynamic Spillover EliminAtion (REDSEA)
  • Spatial lineage tracking using epitope combinatorial tags (Epic)

Sponsored by