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GenomeWebinars

Senior Medical Consultant, University Hospital Brugmann, Université Libre de Bruxelles

This webinar will discuss data from a recent real-world comparison study evaluating performance of two cell-free DNA methodologies as first-line prenatal screens.

Rapid global adoption of noninvasive prenatal testing (NIPT) by cell-free DNA analysis into clinical care has led to a growing number of technical approaches and menu options. With increasing frequency, the commercial availability of a test greatly precedes the presentation of peer-reviewed data evaluating performance and clinical utility, making it difficult for clinicians to differentiate how the test may impact clinical care. In order to provide high-quality patient care, laboratories and clinicians must have access to evidence that allows critical evaluation of testing options.

In this webinar, Dr. Elisa Bevilacqua of Brugmann University Hospital will present data from a recent study evaluating two cell-free DNA tests as first-line prenatal screens in Belgium: a genome-wide massively parallel sequencing test and a targeted Harmony Prenatal test performed in a local clinical laboratory.

Dr. Bevilacqua will describe results comparing sensitivities, false positive rates, failure rates, and turn-around-times, and discuss the clinical utility of additional findings beyond the common trisomies revealed by genome-wide cell-free DNA analysis.

Sponsored by
Thu
Mar
26
11:00 am2020
Sponsored by
Horizon Discovery

Using CRISPR/Cas9-based Gene Targeting to Study Cell Biological Processes

GenomeWebinar

Professor of Biology,
Whitehead Institute for Biomedical Research,
Department of Biology, MIT

A key goal for cell biological analyses is to assess the phenotypes that result from eliminating a target gene. For the past 25 years, the predominant strategy utilized in human tissue culture cells has been RNAi-mediated protein depletion. However, RNAi suffers well-documented off-target effects as well as incomplete and reversible protein depletion. The implementation of CRISPR/Cas9-based DNA cleavage has revolutionized the capacity to conduct functional studies in human cells.

In this webinar, Dr. Iain Cheeseman of the Whitehead Institute for Biomedical Research will describe the strategies that his lab utilizes to analyze the cell biological phenotypes resulting from gene inactivation in human cells using Cas9-mediated gene knockouts.

First, he will discuss an inducible knockout strategy using modified cell lines with a doxycycline-inducible version of Cas9 and a stably expressed single guide RNA (sgRNA) introduced using a lentiviral vector. The inducible and conditional nature of the Cas9 induction allows a researcher to elucidate the consequences of both acute and chronic elimination for a target gene, which is particularly critical when analyzing genes required for cellular fitness, including essential genes. Using this strategy, the Cheeseman lab has generated and characterized a broad collection of inducible CRISPR/Cas9 knockout human cell lines targeting diverse cell cycle and cell division processes.

Second, Dr. Cheeseman will discuss alternate strategies for the effective introduction of the Cas9 guide RNA into target cells using synthetic guide RNA transfection. He will compare the efficiency of synthetic sgRNA and crRNA guides with that of cell lines stably expressing lentiviral-delivered RNA guides and will discuss technical considerations for effective use of synthetic guides for cell biological phenotypes.

Finally, Dr. Cheeseman will discuss strategies to conduct Cas9-based targeting for cell biological phenotypes at a larger scale, towards enabling genome-wide phenotypic screens. Together, these strategies provide a robust, flexible, and scalable approach for conducting functional studies in human cells.

Sponsored by

Project Scientist, Department of Microbiology, Immunology and Molecular Genetics, University of California

Technology Co-Inventor , IsoPlexis

This webinar will discuss the application of single-cell proteomics and immune-imaging in adoptive cell therapy (ACT) for cancer.

Interleukin-2 (IL-2) is a component of most protocols of ACT, but it is limited by short exposure and high toxicities. NKTR-214 is a kinetically engineered IL-2 receptor βγ-biased agonist designed to preferentially activate and expand effector T and natural killer cells over regulatory T cells in the tumor.

In this webinar, Giulia Parisi of the University of California, Los Angeles, will discuss the use of in vivo immuno-imaging to track the biodistribution of the adoptively transferred T cells in relation to anti-tumor efficacy. She will also discuss how this study used single-cell proteomics and functional biomarkers to characterize the functional phenotype of the cell subsets modulated by ACT+NKTR-214.

The objectives of this seminar are to:

  • Provide an overview of the use of an engineered IL-2 receptor agonist in adoptive cell transfer protocols
  • Present methods to track T cell anti-tumor activity and in vivo biodistribution
  • Describe the application of single-cell functional proteomics in identifying biomarkers in next-generation therapies
Sponsored by
Tue
Apr
7
12:00 pm2020
Sponsored by
Agilent

Application of Target Enrichment to Pathogen Genomics and Transcriptomics

GenomeWebinar

Professor of Virology, Division of Infection and Immunity, University College London & Great Ormond Street Hospital for Children

 

Target enrichment has been shown to be more sensitive than metagenomic methods and PCR amplicon sequencing for pathogen genomes, and faster than traditional methods for analysis of hard to culture pathogens, for example viruses and some bacteria.

In this webinar, Judith Breuer of University College London & Great Ormond Street Hospital for Children will show how Agilent’s SureSelect targeted enrichment technology:

  • Allows her team to generate high quality consensus sequences and preserves the population structure of minority variant sequences compared to sequencing directly from clinical samples.  
  • Enables them to interrogate clinical samples for better understanding of the evolution of drug resistance and pathogen transmission. 
  • Offers a useful tool study the impact of drugs on pathogens and the recovery of pathogen transcriptomes as part of understanding pathogenesis.

For Research Use Only. Not for use in diagnostic procedures.

Sponsored by
Recent GenomeWebinars

Science Leader,
National Measurement Laboratory at LGC 

Since the publication of the “The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments” (dMIQE) in 2013, there has been a large expansion of the applications of dPCR such as single nucleotide variations (SNVs) and copy number variations (CNVs) measurements associated with disease diagnostics. At the same time, international measurement organisations, such as the National Measurement Laboratory (NML) at LGC, have been working towards the development of molecular methods that are SI traceable to support the translation of these applications into the clinic. Digital PCR has the potential to be a traceable method as the concentration of a target is calculated based on the proportion of target-positive partitions and the application of Poisson statistics.

This webinar will focus on the use of dPCR for quantifying gene CNVs frequently used in diagnosis and selection of targeted therapy. Using models, like the HER2 gene in breast cancer, we will investigate the ability of dPCR to measure small changes in the gene copy number with further work to develop methods to counteract the measurement bias that can be caused by linked target copies in the sample. The talk will also highlight key dPCR performance parameters considered in the updated version of the dMIQE guidelines thereby fostering dPCR best practice and the use of dPCR as a gold standard approach.

Sponsored by

Lab Director, Clinic for Special Children

 

Senior Vice President, AutoGen

This webinar will explain how the Clinic for Special Children in Strasburg, Pennsylvania, has transformed its DNA workflows to improve the diagnosis and treatment of genetic illnesses that are prevalent in the pediatric population of its community.

Dr. Erik Puffenberger, lab director at the clinic, will discuss how the organization improved its genetic workflows in order to give patients the best care possible and provide better outcomes for families. Dr. Puffenberger will share details of how the clinic, as a small, specialized organization, balances the desire to adopt new technologies with the realities of working with a limited budget.

One of the many diseases the clinic diagnoses and treats is spinal muscular atrophy (SMA). The occurrence of SMA is much higher within the community the clinic serves, comprising Amish and Mennonite populations, than in the general population. This webinar will highlight how the clinic has evolved its DNA workflows to improve clinical outcomes for SMA and other diseases.

Dr. Puffenberger will detail the DNA extraction technologies that have allowed the clinic to improve its workflows and will also discuss the promise of cell-free DNA for non-invasive prenatal diagnosis and treatment.

Webinar participants will learn about the following areas:

  • How to optimize the workflow in a clinical environment to diagnose and treat genetic illnesses
  • Which sample types provide the best chances for a positive clinical outcome
  • New ways automation enables non-invasive prenatal diagnosis and treatment
Sponsored by

Professor of Pathology,
University of Pittsburgh

This webinar will discuss a study that used long-read, single-cell and probe capture based transcriptome sequencing to explore the distribution of isoforms in colon cancer samples and their metastasis counterparts.  

The complexity of mammalian gene expression involves the combinatorial use of exons during RNA splicing. The selective splicing process generates a plethora of isoforms per gene and accounts for what is arguably the largest source of variation in transcriptome diversity and adaptability. However, the quantification of the diversity of mammalian transcriptome is impeded by the lack of accurate, quantitative, and affordable long-read isoform sequencing.

Accurate analyses of the distribution of isoforms, fusion gene isoforms, and point mutation isoforms remains a huge challenge for human malignancies. In this webinar, Jianhua Luo of the University of Pittsburgh will discuss a study that used the ability to capture transcripts from user-defined sets of genes together with synthetic long-read sequencing of full-length mRNA to characterize the long-read transcriptomes from three pairs of colon cancers and their metastasis counterparts.

Dr. Luo will share how the study demonstrated a unique pattern of RNA isoform redistribution and enrichment for specific mutated isoforms and fusions in metastatic cancer cells in comparison with their primary cancer counterparts. The isoform switching and mutation-enriched isoforms are predicted to have subtle effects on protein structure, which may differentially impact protein signal transduction and response to drug treatment.

The results demonstrate that the use of probe capture and long-read sequencing provides focus and granularity that was previously inaccessible in transcriptome analysis of both bulk and single cell samples. Full-length transcriptome analysis may be essential for our understanding of gene expression regulation in human cancers.

Sponsored by
Thu
Feb
20
11:00 am2020
Sponsored by
Thermo Fisher Scientific

Advances in NGS Gene Expression Studies to Reduce The Cost of Sequencing

GenomeWebinar

Assistant Professor, Division of Microbiology, Tulane University

Senior Global Marketing Manager, Thermo Fisher Scientific

This webinar discusses the use of 3’ mRNA sequencing to reduce the cost of gene expression studies on Illumina NGS systems.

Focusing on a study that used peripheral blood mononuclear cells from pregnant macaques acutely infected with Zika virus, Dr. Nicholas Maness of Tulane University discusses the pros and cons of 3’ mRNA sequencing compared to whole-transcriptome sequencing for gene expression studies. He details the differences in the data collected and the costs of each approach and offers suggestions on when to use each method.

This webinar is a must-see for anyone seeking to reduce the cost of sequencing from gene expression studies or who wish to perform pilot studies inexpensively.

Cris Kinross of Thermo Fisher Scientific provides an overview of the differences between 3’ mRNA-seq, mRNA-seq, and whole-transcriptome sequencing.

 In this webinar, you learn how to:

  • Reduce the cost of NGS gene expression studies
  • Consider if 3’ mRNA sequencing or whole-transcriptome sequencing meets the needs of your project
  • Obtain answers more quickly using smaller data sets
Sponsored by
Wed
Feb
19
1:00 pm2020
Sponsored by
Horizon Discovery

CRISPR-directed Gene Editing in Human Cells: What You Get Is More Than What You Want

GenomeWebinar

Founder and Director of the Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute at ChristianaCare

Product Manager – Gene Editing Reagents, Horizon Discovery

The breakthrough technology CRISPR/Cas has revolutionized molecular approaches to the treatment of disease and provided opportunities for the development of clinically relevant gene therapies. While a wealth of information surrounding gene knockout in human cells is now in hand, we are only beginning to appreciate the intricacies and genetic outcomes resulting from reactions where the aim is to correct a mutation or precisely tag a specific sequence in the genome.

The most well-known method for gene repair is homology-directed repair (HDR), a heterogeneous series of pathways whose activity lead to precise and imprecise genetic alterations. Some pathway activity can lead to unwanted changes.

In this webinar, Eric Kmiec, founder of the Gene Editing Institute at ChristianaCare, will discuss the global distribution of genetic outcomes as a function of CRISPR-directed gene editing, highlighting in vitro and in vivo systems that enable such visualization.

An appreciation for the heterogeneity of HDR products in a whole cell population is becoming essential as therapeutic applications of gene repair advance toward the clinic.

Sponsored by
Wed
Feb
5
1:00 pm2020
Sponsored by
LGC

Development of a Novel Multiplex Assay: A Partnership Case Study

GenomeWebinar

Senior Scientist, R&D Group, Co-Diagnostics 

Head of Business Development, Co-Diagnostics

General Manager, Magna Mosquito Abatement District

This webinar provides a behind-the-scenes look at the collaborative development of a novel multiplex assay to speed detection of mosquito-borne illness in the clinical setting.          

A pivotal part of the molecular diagnostics innovation chain that is often overlooked is the relation between critical component suppliers, test manufacturers, and end users. This webinar addresses the development and utility of an innovative multiplex application for detection of Zika, dengue and chikungunya in mosquitos, enabling communities to reduce infection rates by vector control and prevent unnecessary infections and subsequent treatments.

Dr. Jana Kent, Senior Research Scientist from Co-Diagnostics (CoDx), will introduce the company’s CoPrimer technology, which provides flexibility in multiplex assay design without cross-reactivity or non-specific amplification (i.e. primer dimers). She shares insights on the development process of the Zika, dengue and chikungunya test and highlight best practices when working with critical component suppliers and end users.

Next, Ryan Lusty, General Manager of the Magna Mosquito Abatement District in Utah, discusses the implementation of this test in his county and how it impacted healthcare outcomes. Ryan discusses the importance of same-day test results for vector control, as opposed to waiting several days for state lab results.                    

Joseph Featherstone from CoDx wraps up by addressing the importance of partnership for the success of innovation, development, and commercialization of molecular diagnostics and will present opportunities for new research and commercial applications.

Sponsored by

Pathologist,
Moffitt Cancer Center

This webinar will discuss how Moffitt Cancer Center has implemented a new capture-based application to accurately assess myeloid malignancies by detecting complex variants in challenging genes in a single experiment.  

Molecular profiling by next-generation sequencing (NGS) of myeloid tumors has become a routine part of disease management. One of the difficulties and limitations of NGS technology has historically been the inability to reliably detect mutations in certain GC-rich gene regions (such as the CEBPA gene) and insertions/deletions in genes such as FLT3, NPM1, and CALR. 

Many labs have circumvented these limitations by performing parallel orthogonal testing, which is redundant, costly, and inefficient. Furthermore, in late 2018, the US Food and Drug Administration approved a targeted therapy for FLT3-mutated acute myeloid leukemia, making accurate and reproducible mutation detection of paramount importance for guiding treatment.

In this webinar, Dr. Mohammad Hussaini of the Moffitt Cancer Center will discuss development of a comprehensive solution that captures 98 genes noted to be of importance in myeloid disease. In particular, he will describe:     

  • The process of evaluating and implementing this new capture-based NGS solution 
  • The accurate detection of challenging genes such as FLT3, CALR, and CEBPA 
  • The global analytical performance of this solution
Sponsored by

VP of Research and Development, NeoGenomics

This webinar will provide a first-hand look at how a clinical lab evolved its tumor profiling workflow from a targeted panel approach toward comprehensive genomic profiling.  

Cancer is a highly complex disease and understanding the various alterations that together determine mechanisms of disease onset, progression, recurrence, and response to treatment is not trivial. These alterations, however, are not all found at the DNA level. Multimodal approaches can generate a profile of these various alterations, but this approach requires a fragmented and challenging workflow.

More recently, the field has started moving toward comprehensive genomic profiling (CGP), enabling a snapshot of the genetic makeup of the tumor at a specific timepoint. This approach provides insights beyond mutations at the nucleotide level that may provide a better understanding of the state of the disease and the various pathways that modulate its progression and response to its environment, including treatment.

In this webinar, Vincent Funari of NeoGenomics will discuss how his team has evolved its profiling approaches for both heme and solid tumors from targeted panels to more comprehensive genomic profiling.

Dr. Funari will highlight tools that enable a more streamlined path for adopting CGP, enabling operational efficiencies such as reduced overall cost while delivering high-quality data. He will also share additional insights his team gained into alterations that were previously missed due to limitations of current technologies.

Sponsored by

Lecturer & RNAi Facility Screening Manager,
Genomic Approaches to Drug Discovery MSc Lead,
The University of Sheffield

Product Manager,
Horizon Discovery

This webinar will provide an overview of high-throughput RNAi screening from the perspective of a dedicated RNAi screening facility.

The use of reverse genetics, such as RNAi, in large-scale functional genomics has been an important tool in gene discovery. Since the beginning of the century, Drosophila, C. elegans and human genomes have been systematically investigated, using RNAi, to probe important biological processes. RNAi has become both practical and routine in cell culture, due to bulk liquid handling, automated data acquisition and processing.

The Sheffield RNAi Screening Facility has been functional for more than 10 years, initially performing Drosophila melanogaster screens and later human.

This presentation will include the aspects of building a screening platform, uses of automation, designing robust screens, experimental controls, and hit validation.

Sponsored by
Tue
Dec
17
10:00 am2019
Sponsored by
Thermo Fisher Scientific

Non-Invasive Characterization of Solid Tumors via NGS Liquid Biopsy Testing

GenomeWebinar

Co-Director, Solid Tumor and Constitutional Disease Diagnostic Laboratory,
University of Navarra

This webinar reviews how liquid biopsy can be considered as an alternative and non-invasive method to tissue biopsy for cancer molecular characterization.

Liquid biopsy enables the study of tumor-specific circulating components, including circulating tumor cells (CTCs), circulating cell-free tumor DNA (ctDNA) and RNA (ctRNA). The approach brings both great potential and new challenges to precision medicine.

This webinar highlights two key aspects of successful implementation of liquid biopsy in the laboratory: proficiency testing and interlaboratory comparison. Additionally, our speaker, Dr. Gorka Alkorta-Aranburu of University of Navarra, discusses specifics of the liquid biopsy methodology, including properties of cell-free nucleic acids and considerations for next-generation sequencing technology.

Learning objectives:

  • The benefits of liquid biopsy as a non-invasive method to better understand cancer development and treatment.
  • The advantages (and challenges) of an NGS approach to study circulating cell-free nucleic acids for clinical applications.
Sponsored by

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