GenomeWebinars

Tue
Jun
19
1:00 pm2018
Sponsored by
Advanced Cell Diagnostics

RNA in situ Hybridization: The Next Generation of Immunohistochemistry?

GenomeWebinar

Director of Anatomic Pathology, Department of Laboratory Medicine,
Geisinger Health System

Chief Medical Officer,
Advanced Cell Diagnostics

This webinar provides evidence for the use of RNA in situ hybridization (RNA ISH) as a replacement for immunohistochemistry (IHC) in cancer research and diagnostic applications.

IHC is the gold standard for many diagnostics, but the approach has some shortcomings, including low diagnostic sensitivity, background staining, unstable antibodies, no available antibodies and a multitude of staining protocols.

RNA ISH has the ability to overcome these problems with IHC and has the potential to address issues with other technologies, including molecular “grind and bind” methods such as PCR, next-generation sequencing and gene expression profiling. The RNAscope RNA ISH method from Advanced Cell Diagnostics uses a brightfield in situ hybridization-based assay to visualize cellular RNA in formalin-fixed, paraffin-embedded tissue sections. The highly sensitive assay shows promise for detecting biomarkers that are missed by other methods.

In this webinar, IHC expert Fan Lin of Geisinger Health System reviews the common applications of RNA ISH in anatomic pathology, discusses how to interpret RNA ISH results and touches on the potential pitfalls of RNA ISH.

Sponsored by
Wed
Jun
20
11:00 am2018
Sponsored by
PerkinElmer

Expert Tips on Sequencing and Library Prep from the Wellcome Sanger Institute

GenomeWebinar

Senior Staff Scientist - R&D Sequencing, Wellcome Trust Sanger Institute

In this webinar, Michael Quail of the R&D Sequencing team at the Wellcome Trust Sanger Institute will provide an expert perspective on library prep for next-generation sequencing. 

The Sanger Institute is a large-scale biomedical research and genome center funded by the Wellcome Trust. The institute was an early adopter of Illumina sequencing technology and was one of the first labs in the world to automate library prep. 

Dr. Quail will discuss problems and biases that can occur during NGS library prep and ways to avoid them. He will review the various steps in sequencing library construction and discuss how biases in genomic content and sample representation can arise in sequencing libraries. 

Dr. Quail's presentation will include recommendations on how to avoid such biases, resulting in more even sequence coverage and fewer samples with insufficient coverage for meaningful analysis.

Sponsored by
Thu
Jun
21
1:00 pm2018
Sponsored by
Roche

Evaluation & Implementation of NGS Liquid Biopsy Assays

GenomeWebinar

Berlin Institute of Health Genomics Core Platform

This webinar will provide a detailed look at how a genomics lab implemented next-generation sequencing (NGS) liquid biopsy assays into its in-house clinical research program.

Interest in liquid biopsy has escalated in recent years due to the minimally invasive sampling method, potential to overcome the challenges of tumor heterogeneity, and the potential for longitudinal monitoring of tumor burden through serial sampling.  Furthermore, the growing adoption of NGS allows more labs to perform NGS liquid biopsy tests in house.

In this webinar, Dr. Tomasz Zemojtel of the Berlin Institute of Health will discuss how his lab implemented Roche's Avenio ctDNA Analysis Kits for in-house clinical research testing. He will discuss:

  • Utility and flexibility of liquid biopsy assays for various research applications
  • Specific parts of the liquid biopsy workflow that are critical for achieving high technical performance and accurate results, such as molecular barcoding and hybrid capture technology
  • Implementation strategy for liquid biopsy assays using artificial plasma samples
  • Data analysis and interpretation

Lastly, Dr. Zemojtel will discuss the data obtained with the Avenio assay workflow from clinical research subjects with ovarian cancer.

Sponsored by

National Cancer Institute, Center for Cancer Research

This webinar outlines a study that sought to characterize the landscape of alternative polyadenylation (APA) in the lung cancer transcriptome in order to gain insight into the role of APA in cancer progression.

APA involves the selection of an alternate poly(A) site on the pre-mRNA that leads to generation of isoforms of various length. In cancer, APA is emerging as an alternative mechanism for proto-oncogene activation in the absence of somatic mutations. Recent studies show a correlation of APA profiles with cancer prognosis, suggesting that APA is an important mechanism of cancer progression. In addition, environmental exposures such as temperature and exogenous hormones can also induce APA as a stress-response mechanism.

In this webinar, Dr. Adriana Zingone of the National Cancer Institute, Center for Cancer Research will discuss her team's work to characterize APA in the lung cancer transcriptome and to test a hypothesis that smoking modulates differential usage of polyadenylation sites within mRNA transcripts.

Sponsored by
Wed
Jun
27
1:00 pm2018
Sponsored by
Roche

Clinical Utility of Liquid Biopsy for Targeted TKI Therapy in NSCLC

GenomeWebinar

Chair, Solid Tumor Oncology and Investigational Therapeutics, Donald S. Kim Distinguished Chair for Cancer Research, Levine Cancer Institute, Atrium Health

Director of Molecular Pathology, Carolinas Pathology Group

This webinar will present data from the Flaura trial and show the clinical utility of liquid biopsy in identifying non-small-cell lung cancer (NSCLC) patients who may benefit from targeted TKI therapies. .

Recently, the US Food and Drug Administration approved AstraZeneca's Tagrisso (osimertinib) for first-line treatment of patients diagnosed with advanced NSCLC whose tumors have epidermal growth factor receptor (EGFR) exon 19 deletions or exon 21 L858R mutations. This approval expanded the options for clinicians to use tyrosine kinase inhibitors to treat their patients with newly diagnosed EGFR-mutated NSCLC.

In parallel to this approval, the FDA also approved expanded indications for the use of the cobas EFGR Mutation Test v2 as a companion diagnostic to Tagrisso with either tumor tissue or plasma.

This webinar will review the key findings from the Phase III FLAURA trial that supported these approvals. Additionally, as lung cancer has been at the forefront for liquid biopsies, this webinar will present data supporting the clinical utility of liquid biopsy in providing patients with a) a non-invasive alternative to a traditional tumor biopsy when no tissue is available, and b) faster time to results about their tumor mutation status, thus allowing physicians to initiate targeted therapy expeditiously when warranted.

Sponsored by
Thu
Jun
28
1:00 pm2018
Sponsored by
PerkinElmer

An Optimized NGS Workflow for Human Metagenomic Analysis

GenomeWebinar

Senior Scientist, Genomic Applications Department, Illumina

This webinar will review a standardized, high-throughput, and fully automated library prep protocol for human metagenomic analysis. 

The human gastrointestinal tract hosts up to 100 trillion microbes with the greatest numbers residing in the distal gut. Given the vast presence of microbial genetic information, the ability to characterize communities from fecal material via next generation sequencing (NGS) has revolutionized the understanding of the human microbiome, and its influence on health. In order to gain further insight on these influences, the need for a standardized and scalable NGS metagenomics protocol is needed to minimize inconsistencies among existing methods (sample collection, sample storage conditions, experimental design, and scalability), which typically lead to data disparities and misrepresentation of the true state of the human microbiome.

In this webinar, Dr. Agata Czyz of Illumina's Genomic Applications Department will discuss a comparative metagenomics study that relied on a high-throughput and automated library prep protocol for stool. Dr. Czyz will discuss several parameters and methodologies that her team tested as well as the key findings of the study.

Sponsored by

Founder, AdvaGenix

This webinar offers a look at how an advanced genetics laboratory implemented and validated a commercial bioinformatics system to help scale its operations. 

William Kearns, founder of genetics testing lab AdvaGenix, will share his team's experience as it sought to increase its testing throughput while maintaining high quality standards. After studying the time and cost associated with building and validating a bioinformatics platform from scratch, as well as the cost of maintaining such a system, the AdvaGenix team decided to look for commercial solutions. 

AdvaGenix needed a solution that adhered to society guidelines and also included domain expertise in genetic testing. The team ultimately opted for a system from Qiagen and has since been able to scale up its operations by at least 25-fold.  Dr. Kearns will discuss his team's experience and learnings from this implementation and the results they have seen so far.

Sponsored by

VP of Clinical Affairs, Veritas Genetics

Founder, Genomenon

This webinar will discuss an approach for automating variant classification based on the American College of Medical Genetics and Genomics guidelines.

Variant interpretation presents a bottleneck for many labs, posing a challenge to the broader adoption of precision medicine. The ACMG/AMP variant classification framework has provided a foundation for this process, but several key obstacles remain. In particular, the identification and prioritization of key publications presents a time- and resource-intensive challenge for many labs.

Join this webinar for a discussion on how Veritas Genetics collaborated with Genomenon to develop a new Literature Classification Tool within the Mastermind Genomic Search Engine to address these challenges.

The speakers will demonstrate:

  • How to more efficiently identify and prioritize publications by ACMG variant classification guidelines
  • How increased specificity and immediate access to annotated search results accelerates variant interpretation workflow
  • How increased sensitivity in literature search results in fewer false negatives

The speakers will discuss promising Veritas trial results that point to a better and faster variant interpretation workflow using the new Literature Curation tool in the Mastermind Genomic Search Engine.

Sponsored by

Principal Investigator of the Laboratory of Functional Neurogenomics, University of Miami, Miller School of Medicine

This webinar will discuss a project that is analyzing the “Human Brainome” – genome, transcriptome, proteome, and phenome interaction data -- to gain insights into Alzheimer’s disease pathogenesis.

Amanda Myers of the University of Miami Miller School of Medicine will describe the study, which used two separate sets of human brain tissue for analysis. Genome, transcriptome and proteome data was collected and analyzed to determine key drivers for Alzheimer’s pathology. Both an analysis of single effects (DNA driving downstream expression of one target) as well as multi-target analysis (transcript and peptide networks) was performed. 

From a set of ~ 5.2 million SNPs, ~15,000 transcripts and ~2000 peptides a small subset of targets was discovered that are computationally predicted to be crucial to disease processes and replicated between our two sets of tissues. Targets were validated in the wet lab to insure that these targets on their own had effects on the specific Alzheimer’s disease brain pathology. Several targets on their own effected disease processes, demonstrating that our pipelines are robust and nominating these targets as new Alzheimer’s disease candidate genes.

 

For more information on other webinar in this series, click here.

Sponsored by
Thu
Jul
19
11:00 am2018
Sponsored by
Thermo Fisher Scientific

Advances in NGS for Ultra-High Sensitivity Applications in Translational and Clinical Research

GenomeWebinar

Co-founder & Chief Technology Officer, Amplexa Genetics

 

This webinar will discuss how ultra-highly sensitive and customizable targeted next-generation sequencing panels are applied in inherited disease research. In particular, the seminar will highlight a study that sought to test the hypothesis that causative genetic variants for inherited diseases that often fall into the category of “de novo mutations” are sometimes the result of undetected mosaicism in the parents.

In this webinar, Hans Atli Dahl, co-founder and chief technology officer at Amplexa Genetics, will share how this study led to the evaluation of the coming soon Ion AmpliSeq HD* targeted NGS solutions from Thermo Fisher Scientific. He will share details of how the Ion AmpliSeq HD* panels address the need for ultra-high sensitive detection and its potential to deliver new insights about the causes of these types of genetic diseases.

Amplexa Genetics, based in Denmark, specializes in clinical genetic testing and clinical variant interpretation associated with a variety of disorders. The company has a long history of NGS analysis in epilepsy and other encephalopathies and recently moved into molecular genetics of endocrine disorders and direct-to-consumer testing for recessive inheritance risk-assessment.

 

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

*The content provided herein may relate to products that have not been officially released and are subject to change without notice.

Sponsored by
Wed
Jul
25
1:00 pm2018
Sponsored by
Streck

Antibiotic Gene Surveillance: What You Don’t See Can Hurt You!

GenomeWebinar

Professor & Director, Center for Research in Anti-Infectives and Biotechnology. Department of Medical Microbiology and Immunology, Creighton University

This online seminar will discuss the advantages of incorporating molecular testing into the microbiology laboratory to aid in the identification of relevant antibiotic resistance mechanisms. 

Surveillance of resistance mechanisms, hospital infection control, and epidemiology require accurate detection of extended-spectrum beta-lactamases (ESBLs), AmpC beta-lactamases, and carbapenemases. For example, an important aspect of infection control is to determine how resistance is spread. Is the spread of resistance due to a clonal outbreak or the movement of mobile genetic elements?

The majority of ESBLs and relevant carbapenemases are encoded on mobile genetic elements; however, AmpC production can be either chromosomal- or plasmid-mediated. Several phenotypic methodologies have been developed to address the detection of beta-lactamase genes, but few can detect the production of AmpC, and none can discern the difference between a chromosomal and plasmid-mediated AmpC producer. Furthermore, a major concern for infectious disease personnel is the inability to detect ESBLs in the presence of AmpC production.

Molecular techniques are required to determine the presence of multiple beta-lactamases within a single isolate or to discriminate between different types of beta-lactamases leading to similar beta-lactam susceptibility patterns. In addition, resistance mechanisms are emerging to other antibiotic classes. The challenge for the infectious disease community is to determine when and if to use molecular testing to aid in the identification of relevant resistance mechanisms, especially when encountering complex susceptibility patterns.

This seminar will highlight the most relevant beta-lactamases and the challenges facing the incorporation of molecular testing into the laboratory. Targets in addition to beta-lactamase genes will also be discussed.

Sponsored by

Graduate Student, University of California, Santa Cruz

Graduate Student, University of Washington

Research Technician, Stowers Institute for Medical Research

This webinar will provide an overview of recent advances in single-cell RNA sequencing from the perspectives of three research organizations.

Our first speaker, Ashley Byrne of the University of California, Santa Cruz, will discuss a long-read cDNA sequencing approach based on Oxford Nanopore sequencing technology to evaluate RNA isoform diversity in single B cells.

Using this approach, Byrne and colleagues have been able to reconstruct isoform-level transcriptomes using their analysis pipeline Mandalorion. They also discovered that much of the RNA isoform diversity observed is found across B cell-specific receptors, which could have implications for immunotherapy design — specifically for targeting B cell lymphomas.

Next, Junyue Cao of the University of Washington will share a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei.

Cao's team used the method, called sci-RNA-seq (single cell combinatorial indexing RNA sequencing) to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 stage, which is over 50-fold “shotgun cellular coverage” of its somatic cell composition. Cao will discuss how the data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.

Our third speaker, Kate Hall of the Stowers Institute for Medical Research, will share two different workflows her team has developed to streamline single-cell RNA-seq services.

The first workflow uses the Single Cell Chromium Controller from 10X Genomics and allows thousands of cells to be pooled together and processed as a single reaction. The high-throughput nature of this method can help identify unique cell populations in a given pool. The second workflow uses the Mantis small-volume pipetting robot from Formulatrix to set up quarter-sized reactions for cDNA synthesis on individual cells. This workflow is more suitable for a smaller sample set as it can help give a more detailed view of specific cell types via full-length transcript sequencing.

For more information on other webinar in this series, click here.

Sponsored by

Oxford Nanopore Technologies is looking into dual listings in London and Hong Kong, according to the South China Morning Post.

The New York Times looks into medical research funding in the US and how the grant system might not be funding the best work.

US lawmakers proposed increasing the National Science Foundation budget, including its facilities account, Science reports.

In PNAS this week: effects of gene deletions on bacterial metabolic networks, genetic responses to sea star wasting disease, and more.