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GenomeWebinars

Tue
May
31
4:00 PM
US Eastern

Sponsored by SomaLogic

Developing Microbiome-Directed Therapeutics for Treating Childhood Undernutrition

Human postnatal development is typically viewed from the perspective of our ‘human’ organs. As researchers come to appreciate how microbial communities are assembled following birth, there is an opportunity to determine how this microbial facet of our developmental biology is related to healthy growth as well as to the risk for and manifestations of disorders that produce abnormal growth.

In this webinar, Jeffrey I. Gordon and Michael J. Barratt of the Washington University School of Medicine will discuss their investigations into the hypothesis that perturbations in the normal development of the gut microbiome are causally related to childhood undernutrition, a devastating global health problem whose long-term sequelae, including stunting, neurodevelopmental abnormalities, plus metabolic and immune dysfunction, remain largely refractory to current therapeutic interventions. The journey to preclinical proof of concept and the path forward to clinical proof of concept emphasize the opportunities as well as the experimental and analytic challenges encountered when developing microbiota-directed therapeutics.

Learning objectives:

  • Understand evidence that impaired postnatal development of the gut microbiota is causally related to childhood undernutrition.
  • Understand how preclinical gnotobiotic animal models can be used to develop new microbiota-directed therapeutics.
  • Understand how multiomic methods, including SomaScan proteomics, can be used to judge the efficacy and mechanism of action of these therapeutics in clinical studies.

Sponsored by

Wed
Jun
01
12:00 PM
US Eastern

Sponsored by Ionpath

Proteomic Characterization of the Tissue Microenvironment with Multiplexed Ion Beam Imaging (MIBI)

Characterization of the cellular composition and spatial organization of the tissue microenvironment has been limited by the techniques available to image the necessary number of biomarkers for broad phenotyping at a subcellular scale.

Multiplexed ion beam imaging (MIBI) combines time-of-flight secondary ion mass spectrometry (ToF-SIMS) with metal-labeled conventional antibodies to image over 40 biomarkers in situ in a single scan at subcellular spatial resolution.

In this webinar, Tomer-Meir Salame, staff scientist in the life sciences core facilities of the Weizmann Institute of Science, will present the MIBI platform and explain its workflow from the perspective of a core facility, providing insight into how this imaging method can be used for studies that require high-dimensional and deep characterization of tissue microenvironments.

MIBI enables quantitative, full periodic table coverage across a five-log dynamic range, imaging all labeled antibodies simultaneously with fields of view up to 800 μm × 800 μm at resolutions down to 350 nm and sensitivities approaching single-antibody detection. MIBI analysis can be performed on FFPE, fresh, or frozen tissue.

Salame will illustrate the platform’s capabilities through a cohort of clinical tissue sections taken from a case study focusing on the characterization of the microenvironment of sentinel lymph nodes in relation to melanoma metastasis.

Sponsored by

Tue
Jun
07
1:00 PM
US Eastern

Sponsored by Agena Bioscience

Using a Mass Spectrometry-Based Platform to Perform Population-Based Newborn Screening for Cystic Fibrosis in the State of Illinois

Cystic fibrosis (CF) is a genetic disorder that mainly affects the respiratory and digestive systems, resulting in a variety of symptoms, including difficulty breathing, infertility, and poor growth in children. Fortunately, CF can easily be diagnosed through newborn screening. When diagnosed early, patients can avoid most of the severe adverse effects. The current methodology for CF screening minimally involves the detection of 23 different disease-causing mutations that occur within the CFTR gene, as recommended by the American College of Medical Genetics (ACMG). Many CF newborn screening pipelines use immunoreactive trypsinogen (IRT) levels as a first-tier laboratory test for CF, as high IRT levels indicate potential pancreatic damage and are commonly associated with the disease. Babies with high IRT levels are then typically considered for second-tier CF testing. Various methods have been used to detect CF mutations, including DNA hybridization and sequencing approaches. However, there has yet to be a high-throughput study that has explored the robustness and reliability of a MassArray-based detection system for CF newborn screening.

In this webinar, Vineet Dhiman, laboratory research scientist for the Illinois Department of Public Health, will discuss population-based newborn screening of CF in the state of Illinois using the Agena Bioscience MassArray instrument, which currently has the capacity to detect the heterozygosity status of 72 CF-related mutations. With the implementation of this CF screening approach beginning in March 2018, the CF status of over 10,000 specimens has been successfully assessed using DNA extracted from dried blood spots. Mutations that are part of the ACMG recommended panel as well as other rare mutations have been positively identified. Although some caveats exist with data interpretation and potential for repeat experiments due to the nature of the MALDI-TOF workflow, the Agena MassArray instrument provides a cost-effective option for CF screening assay for newborn screening laboratories.

Sponsored by

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Wed
Jun
15
10:00 AM
US Eastern

Sponsored by SPT Labtech

Developing a Miniaturized DNA-seq Method to Reduce Costs With a Next-Generation Liquid Handling Platform

Advances in sequencing instrument output coupled with the associated reduction in cost per gigabase make it feasible to do studies with larger and larger sample numbers. There is also a push to reduce the cost of genomic experiments to democratize the field and allow more people access. These goals necessitate the need for low-cost library construction techniques. Reaction miniaturization can achieve this by increasing the number of samples that can be prepared per kit. The Earlham Institute offers a low-input Nextera library prep to meet this need. However, the original Nextera chemistry has issues with high-GC content genomes. This reduces the method's effectiveness when dealing with species with high or unknown GC content.

The latest tagmentation library prep kit, Illumina DNA Prep, is also amenable to miniaturization and, in the full reaction version, can cope with high GC content. In this webinar, Thomas Brabbs will present a miniaturized version of the DNA Prep method that was developed in collaboration with SPT Labtech for their new Firefly automated liquid handling platform. He will discuss how human and a mock-bacterial community miniaturized libraries compare to full volume ones. This will focus on genome coverage and GC bias.

Sponsored by

SPT Labtech
Thu
Jun
16
11:00 AM
US Eastern

Sponsored by Mission Bio

Bringing a New Standard of Clarity to Solid Tumor Research With Single-Cell Genomics

A major challenge to combating cancer is the dynamism and inherent heterogeneity contributing to the disease's onset, progression, and relapse. In the enormous efforts to identify the factors underlying these factors, bulk sequencing is widely used, but the need for unmasking the underlying genetic diversity across cell populations remains unmet.

Single-cell DNA sequencing can be used to interrogate clonal mosaicism and neoplastic transformation, metastatic dissemination, and therapeutic resistance with its ability to co-analyze SNVs and CNVs at the single-cell level in a scalable manner. As a tool for probing clonal architecture and evolution, researchers can identify zygosity, mutational co-occurrence, and rare mutations in individual cells.

Jorge Reis-Filho of Memorial Sloan Kettering Cancer Center will share the strategies for characterizing intratumor heterogeneity and evolutionary trajectories in cancers at the single-cell level and present his latest findings in breast cancer research.

This webinar will also present the latest advances in single-cell DNA sequencing, including pre-designed solid tumor DNA panels, single-cell CNV analysis workflow, and nuclei isolation protocols enabling solid tumor researchers to access this technology.

Attendees will:

  • Learn how single-cell DNA sequencing can bring a new level of clarity to research in solid tumors, such as breast cancer, by providing insights into the clonal architecture, mutation co-occurrence, and rare mutations driving tumor progression and therapy resistance.
  • Discover the science behind the Tapestri single-cell sequencing platform.
  • Hear about case studies and implementation considerations, including cell and nuclei prep, panel design, and analysis.

Sponsored by

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Thu
Jun
16
1:00 PM
US Eastern

Sponsored by Qiagen

Virtual Roundtable: Data Curation and AI/Machine Learning in Drug Discovery Informatics Workflows

Pharmaceutical companies and researchers are increasingly turning to artificial intelligence and machine learning to turbocharge and laser-focus their processes on potential drug targets for development. But this technology is only as good as the data that trains the computing algorithms, so data curation is imperative. In this Virtual Roundtable, we will look at what bioinformatics tools and expertise researchers will need for their drug discovery pipelines. We will take a specific look at approaches in data curation, including how bioinformaticians are collecting, harmonizing, curating, and analyzing disparate datasets.

Join us as we hear from four leading experts on the use of AI and machine learning for data curation to support drug discovery informatics workflows. Our panelists will discuss their own work, the methods they have used, and the new possibilities available to researchers in their fields. At the end, we'll have a live question and answer session featuring submissions from our audience.  

Sponsored by

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Fri
Jun
17
2:00 PM
US Eastern

Sponsored by Applied BioCode

A Clinical Lab’s Journey to Gastrointestinal Syndromic Molecular Testing using Barcoded Magnetic Bead Technology

Gastrointestinal (GI) illness (gastroenteritis) is inflammation of the stomach and small and large intestines. The main symptoms include vomiting and watery diarrhea. Infections causing gastroenteritis can be viral, bacterial, or parasitic in origin. Since the spectrum of pathogens that cause GI infections is quite broad, the detection of pathogens typically requires an assortment of approaches (culture, antigen detection, stool parasite microscopy) to identify the causative agent. Multiplex molecular tests enable labs to test at once for several of the most common GI pathogens while providing improved analytical specificity and sensitivity and turnaround times. 

This webinar will discuss a study in which a clinical lab evaluated the Applied BioCode Gastrointestinal Pathogen Panel (GPP) assay, focusing on the four most common bacterial targets as well as virus and parasite targets.

The Applied BioCode GPP assay is an FDA-cleared, high complexity test that detects 17 of the most common GI pathogens including viruses, bacteria, and parasites that cause infectious diarrhea. It is run in a high-throughput 96 well microplate format on the automated BioCode MDx-3000 System, which combines the amplification, hybridization, and detection steps for the assay. The automation of these steps into a single system decreases costs, hands on time, and minimize potential contamination risk.

Sponsored by

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Mon
Jun
20
10:00 AM
US Eastern

Sponsored by Curiox Biosystems

Could Debris Be Masking Your True Results: A Scientist’s Perspective on The Importance of Sample Prep

New single-cell technologies have recently facilitated deeper exploration of inter- and intratumor heterogeneity than previously possible. These innovations are poised to better inform on underlying molecular and cellular characteristics that impact key disease mechanisms such as drug resistance and tumor recurrence. Before any downstream analyses, especially with regards to tumor microenvironment monitoring, cells need to be processed into suspensions that are free of debris and aggregates. Current workflows often fall short of reliably yielding the desired cell types at a high frequency, thereby hampering accurate measurements of tumor-infiltrating leukocytes, including rare immune subsets. Pre-analytical factors have long been neglected when interpreting flow cytometry fit-for-purpose results. However, preserving original cell biology and eliminating interfering debris as much as possible across applications is crucial to overall data quality and reproducibility. It can be achieved by adopting automation solutions such as Curiox's Laminar Wash Technology to ensure better, standardized sample preparation for fluorescence-based assays.

Sponsored by

Curiox Logo
Tue
Jun
21
1:00 PM
US Eastern

Sponsored by Illumina

DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

In this webinar, Peter W. Laird, professor at the Van Andel Research Institute, will discuss the development of a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. Laird will present a comprehensive validation of this array platform and discuss the applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high sample-throughput studies in this important model organism.

Laird and colleagues have dissected DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, the team found that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites.

Sponsored by

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Wed
Jun
22
2:00 PM
US Eastern

Sponsored by Millipore Sigma

Designing, Scaling, and Commercializing In Vitro Diagnostics Based on Disruptive Technologies

From molecular diagnostics based on PCR and next-generation sequencing (NGS) to those incorporating CRISPR, strategies used in the design of in vitro diagnostic (IVD) assays increasingly take advantage of disruptive technologies at the forefront of innovation. This presentation will review the DETECTR technology, a proprietary CRISPR-based detection method developed by Mammoth Biosciences. This presentation will also discuss challenges in the development of diagnostics assays using cutting-edge technology, provide insight into a high-throughput SARS-CoV-2 detection assay based on the DETECTR technology, and highlight the collaboration between the technology developer and contract manufacturer, MilliporeSigma. The result of the successful collaboration is a CRISPR-based diagnostic test that has equivalent performances to PCR but has a shorter turnaround time.

The audience will learn:

  • Strategies in the design of an IVD using disruptive technologies. 
  • How to bring a CRISPR-based diagnostic test to a scaled-up commercialized product.
  • Steps in the scale-up and commercialization of the product.

Sponsored by

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Thu
Jun
23
1:00 PM
US Eastern

Sponsored by Antylia Zeptometrix

Best Practices for Maintaining Quality in Molecular Diagnostic Testing

Molecular diagnostics has quickly become one of the leading global technologies for infectious disease testing. As such, clinicians and physicians rely on the results generated from these tests for accurate patient diagnoses. The field is constantly growing and evolving to meet the demands of infectious disease testing, but what remains constant is the importance for laboratories to maintain rigorous quality management practices, including quality control, to help ensure reliable test results.

With multiple regulatory and accreditation bodies like ISO, CLIA, CAP, and CLSI weighing in on good laboratory and quality practices, it can be challenging to implement a quality management system for your laboratory. This webinar will elucidate the current landscape of considerations for implementing a quality system in laboratories running molecular diagnostic assays, including quality controls.

At the end of this webinar, attendees will be able to:

  1. Describe the relevant regulatory and quality system management principles as they apply to laboratories running molecular diagnostic tests.
  2. Design appropriate quality control strategies for molecular/PCR-based testing methodologies.
  3. Identify tools to help implement effective quality management of molecular diagnostic tests.

Sponsored by

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Wed
Jun
29
11:00 AM
US Eastern

Sponsored by DNA Script

On-Demand Enzymatic Synthesis of Fluorescently Labeled Probes Enables Rapid Optimization of an smFISH Assay for Drosophila A Virus Detection

In collaboration with the Institut Pasteur, on-demand Enzymatic DNA Synthesis (EDS) using the Syntax System accelerated the design-print-test-learn cycle required to optimize smFISH assays for the detection of viral RNA in the gut of Drosophila melanogaster. Sets comprised of 20-48 fluorescently-labeled oligos specific to Drosophila A virus (DAV) and endogenous RNAs were printed in the laboratory using the Syntax System. The results of the study demonstrate that use of same-day enzymatic synthesis to quickly iterate through probe design to fine-tune sensitivity and specificity can accelerate the optimization of smFISH assays as a rapid and simple alternative to immunofluorescence.

Sponsored by

Thu
Jun
30
1:00 PM
US Eastern

Sponsored by Vizgen

Investigating Cellular Targets in Narcolepsy and Other Arousal-Based Disorders with Single-Cell Spatial Transcriptomics and Optogenetics

In narcolepsy, sleep attacks and state instability are caused by the loss of orexin/hypocretin neurons in both animals and humans. However, the cellular and circuit mechanisms by which orexin/hypocretin neurons contribute to consolidated arousal and wakefulness remain unclear.

In this webinar, Roberto De Luca, staff scientist at Beth Israel Deaconess Medical Center, will describe newly revealed long-range and local circuitry that provides a new framework for understanding how pathologic loss of orexin/hypocretin neurons results in the inability to maintain consolidated wakefulness in narcolepsy and suggests a novel cellular target for treating a wide range of arousal-based disorders.

Using a combination of in vivo optogenetics, in vitro optogenetically-based circuit mapping, and single-cell spatial transcriptomics, De Luca and colleagues demonstrated that orexin/hypocretin neurons contribute to arousal maintenance through indirect inhibition of sleep-promoting neurons of the ventrolateral preoptic nucleus (VLPO).

Webinar learning objectives:

  1. Define the neuronal circuits that modulate the VLPO in sleep and wakefulness.
  2. List the key populations in the VLPO that have a pivotal role in sleep and wakefulness.

Sponsored by

Vizgen