Close Menu

Webinar/Video Library

October 29, 2020
Sponsored by
Illumina

How to Train Your DRAGEN for Pathology Informatics

GenomeWebinar

Laboratory Director,
Xing Cancer Care

Illumina’s BaseSpace Sequence Hub (BSSH) supports primary and secondary analysis of massively parallel sequencing data and can be applied to gene panel data that is generated as part of a clinical cancer assay performed in a pathology lab.

In this webinar, Lynn Fink of Xing Cancer Care will discuss how her ISO15189-accredited lab has used BSSH to support informatics data analysis as part its routine testing and will share details of why the lab chose this platform over other options.

In particular, Lynn will share how the lab uses the BSSH-hosted DRAGEN (Dynamic Read Analysis for Genomics) apps — Enrichment, Germline, and Somatic — to perform in-depth coverage analyses of a 1,000 cancer gene panel, germline alteration calling, and tumor-normal paired somatic alteration calling, respectively. These apps support about 95 percent of the lab’s analytical needs.

Sponsored by
GenomeWebinar

Associate Professor and Associate Department Head
Department of Agronomy and Horticulture, University of Nebraska-Lincoln

Director of Operations,
Agriplex Genomics

Director of Genomics Solutions,
NRGene

Molecular breeding methods such as genomic selection and genome-wide association studies often require high-density genotypic data from many samples, but the cost and complexity of genotyping at this scale may be prohibitive.

This presentation will outline three areas for improvement that can be combined for greatest impact: marker optimization, efficient genotyping, and data imputation. 

The challenge with marker optimization is to control cost by minimizing the number of SNPs genotyped yet obtaining an accurate description of each individual genome analyzed and capture the diversity within the breeding germplasm. We will offer methods for minimizing genotyping, allowing the analysis of more individuals, and data imputation generating high density data from sparse genotyping.

The development of a 1K SNP set for genomic selection in soy is presented as an example. The 1,000 soy SNPs were selected to provide maximum informativeness in US North Central Soy public breeding programs. The SNPs were developed into molecular inversion probes, a low-cost genotyping-by-sequencing method. This approach is cost-effective and provides high-quality genotypic data.

This presentation will next discuss PlexSeq, a novel approach for efficient mid-density SNP genotyping. PlexSeq uses artificial intelligence algorithms to create highly multiplexed genotyping assays followed by a unique and effective workflow. This technology has advantages in terms of efficiency and cost.

Next, the webinar will address SNPer, a method of SNP optimization and data imputation in three steps: 1) analysis of the breeding germplasm sequence and haplotype diversity; 2) optimization of SNP targets for genotyping by minimizing the number of targets and maximizing the information gained from each;  and 3) imputation of data at ungenotyped SNP loci. The result is a complete and accurate description of each sample genome.

Sponsored by
October 26, 2020
Sponsored by
Sophia Genetics

Robust CNV Detection Using Whole-Exome Sequencing for Complex Cases

GenomeWebinar

Scientific Director, Chief Genetic Officer, Co-founder
Genotypos Science Labs

This webinar will discuss Genotypos Science Labs’ experience with a whole-exome sequencing solution supporting the detection of copy number variants (CNVs) for the management of complex cases.

CNVs are a well-established cause of human genetic disease. Karyotype and microarray analyses have served as gold standards in molecular diagnostics for CNVs, but the increasing number and complexity of possible genomic changes require more sensitive testing.

Whole-exome analysis is emerging as a reliable tool in the study of genetic disorders and has proven to be particularly effective in identifying disease-associated genes that are refractory to linkage analysis. However, the detection of CNVs in whole-exome analyses presents unique challenges due to the large number of genomic changes present, resulting in noise and biases. Hence there is a need for a tailored and robust analytical solution for the detection and exome-wide analysis of CNVs.

In this webinar, Dr. Pantelis Constantoulakis, Director and Chief Genetic Officer of Genotypos Science Labs, will present his experience with whole-exome sequencing (WES). In particular, he will describe:

  • How WES leads to improved results
  • A streamlined workflow enabling the sensitive detection of CNVs
  • A concrete case of a de novo CNV detection linked to growth retardation and hearing loss
Sponsored by
GenomeWebinar

Assistant Professor, University of Lorraine,
Tumor Molecular Biology Unit, Institut de Cancérologie de Lorraine

This webinar will share the Lorraine Cancer Institute's experience in implementing a novel targeted solution to accurately assess homologous recombination repair (HRR) deficiency by analyzing a series of genes, beyond BRCA, and calling multiple types of variants, including copy number variants (CNVs). In the past, HRR deficiency has been commonly associated with BRCA mutations, but recent evidence shows that HRR deficiency detection should not exclusively focus on BRCA, single nucleotide variants (SNPs), and insertions/deletions (indels).

The Lorraine Cancer Center is currently participating in a guideline-defining multicenter study on ovarian cancer, investigating the correlations between a larger range of genomic alterations linked to HRR, clinical evolution, and therapeutic impact.

Dr. Alexandre Harlé, from the institute's Tumor Biology Unit, will describe the adoption of a next-generation sequencing (NGS) solution for broad HRR-deficiency-analysis, additionally enabling CNV detection. He will discuss:

• Why the institute chose a broad and future-proof HRR-deficiency-analysis approach

• How a single NGS workflow can assess a large range of HRR-related variants

• The methods used to confirm the analytical performance of the solution

• The challenges lying ahead and how can they be solved

Sponsored by
GenomeWebinar

Head of Division of Molecular Diagnostics,
London Health Sciences Centre (LHSC)

Target enrichment has been a major driver behind the clinical adoption of next-generation sequencing (NGS) over the last decade because it simplifies analysis and provides a cost-effective method of massive parallel resequencing. It has not only replaced Sanger sequencing, but it is actively dispensing the need for parallel copy number variant (CNV) analysis using classic techniques.

In this webinar, Bekim Sadikovic of the London Health Sciences Centre will demonstrate the performance of Roche’s new KAPA Target Enrichment technology in custom gene panels.

Dr. Sadikovic’s team has streamlined a clinically validated and robust CNV detection algorithm using targeted NGS gene panel data from the Roche SeqCap EZ platform, which they have used to assess complex genomic regions, including pseudogenic DNA sequences and mitochondrial genome heteroplasmy.

In this webinar, Dr. Sadikovic will share details of his team’s evaluation of the new KAPA technology in custom gene panels, including hereditary oncology, mitochondrial disorders, and Charcot-Marie Tooth disease, by using samples previously tested in his lab.

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

KAPA, HYPEREXOME, and SEQCAP are trademarks of Roche. All other product names and trademarks are the property of their respective owner.

Sponsored by
GenomeWebinar

Scientist – Platform responsible dPCR,
Department of Molecular Diagnostics and Flow Cytometry (MOC), Blood Transfusion Service Zurich, Swiss Red Cross

Field Application Scientist,
Stilla Technologies Europe

This webinar will discuss a new method that relies on Crystal digital PCR from Stilla Technologies to monitor chimerism in patients after stem cell transplantation, which is a key part of surveillance for impending clinical relapse.

The new method relies on target detection by Stilla’s Crystal dPCR with the Naica system. The process allows for single nucleotide variant detection in up to 20,000 partitions per reaction, with up to 48 reactions per run.

Elise Gourri of the Blood Transfusion Service Zurich will discuss the validation and implementation of the Naica system for routine chimerism monitoring.

Her presentation will discuss how the Department of Molecular Diagnostics and Flow Cytometry confirmed the reliability of the dPCR platform on samples from previously monitored patients as well as external quality assessment samples. They could provide reproducible quantification of the minor allele, even below 0.25 percent, and, notably, the clinically required 0.5 percent minor allele sensitivity was achieved with only 5 ng of input DNA.

The webinar will detail the department’s conclusion that the Naica system is fast, convenient, and highly accurate.

Sponsored by
October 15, 2020
Sponsored by
Agena Bioscience

A Comparison of cfDNA Approaches to Guide Targeted Therapy in NSCLC

GenomeWebinar

Professor of Molecular Oncological Pathology
University Medical Center Groningen

Staff Scientist, Scientific Affairs
Agena Bioscience

In non-small cell lung cancer (NSCLC), early detection of emerging resistance mutations such as EGFR T790M is important in order to determine the appropriate targeted therapeutic strategy.

In this webinar, Prof. Ed Schuuring of University Medical Center Groningen will report on a comparison study for the detection of mutations in plasma DNA of NSCLC patients using the Roche Cobas EGFR v2.0 Mutation Test, BioRad droplet digital PCR, and the Agena Bioscience UltraSEEK Lung Panel. Prof. Schuuring will discuss the detection sensitivity of clinically relevant markers across the platforms and will also highlight the relevance of pre-analytical quality and quantity assessment of cfDNA.

Dr. Alexander Sartori from Agena Bioscience will follow with an overview of the MALDI-TOF based MassARRAY System and available mutation panels for both tissue and plasma DNA in various cancers.

Sponsored by
GenomeWebinar

Lower Gastrointestinal Medical Oncology and Trials Lead,
Peter MacCallum Cancer Centre

Circulating tumor DNA (ctDNA) can allow clinicians and researchers to better understand which patients are at high risk of recurrence and should be offered intensified chemotherapy or selected for clinical trials. Those with low-risk disease may be able to avoid chemotherapy and its associated side effects.

Methods for ctDNA detection require very high-sensitivity approaches in order to detect microscopic disease after surgery or treatment. Methods have been developed that utilize genomic profiling of tumor tissue based on patient-specific next-generation sequencing (NGS) panels. High-sensitivity personalized panels allow detection of residual disease and serial monitoring for detection of recurrence.

This webinar will discuss the use of such panels to test for residual disease and recurrence in the treatment of colorectal cancer.

Sponsored by
GenomeWebinar

Principal Investigator, CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences

This webinar will outline the use of targeted protein degradation (TPD) to understand transcriptional processes at a high kinetic resolution.

TPD is a new therapeutic modality based on small molecules, called degraders, that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. The ubiquinated proteins are then degraded by the proteasome. 

In this webinar, Georg Winter of CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, will discuss his team’s efforts to chart the function of the human Mediator complex by combining acute protein ablation with nascent RNA sequencing approaches. 

Dr. Winter will discuss how his team develops phenotypic drug screens to find novel small-molecule degraders that function as “molecular glues,” which can degrade otherwise unligandable proteins by orchestrating direct interactions between target and ligase. 

He will also describe a scalable strategy toward glue degrader discovery that is based on chemical screening in hyponeddylated cells coupled to a multi-omics target deconvolution campaign. This approach led the CeMM team to identify compounds that induce ubiquitination and degradation of cyclin K by prompting an interaction of CDK12–cyclin K with a CRL4B ligase complex. Notably, this interaction is independent of a dedicated substrate receptor, thus functionally segregating this mechanism from all described degraders. 

The presentation will outline a versatile and broadly applicable strategy to identify degraders with nonobvious mechanisms and thus empower future drug discovery efforts.

Sponsored by
GenomeWebinar

As cases of COVID-19 continued to grow this spring and summer in the US, so too did the number of Emergency Use Authorizations from the FDA for clinical diagnostic tests aimed at detecting current and past infections. The agency's policies for granting EUAs for both molecular and antibody tests evolved over time as more was learned about SARS-CoV-2 and its spread, and diagnostics firms and labs needed to adapt to these changes.

Dr. Elizabeth Hillebrenner, associate director for scientific and regulatory programs at the FDA's Center for Devices and Radiological Health, will kick off this virtual roundtable with an overview of the EUA program, how it evolved, and how lessons learned during the current pandemic may shape future policies and actions by the FDA. She will then take part in a panel discussion that will include a variety of stakeholders from the diagnostics and clinical lab industries. Panelists will include Dr. Robert Boorstein, Medical Director of Lenco Diagnostic Laboratories; Danelle Miller, VP, Global Regulatory Policy and Intelligence for Roche Diagnostics; Dr. Jeffrey Klausner, Professor of Medicine and Public Health at UCLA David Geffen School of Medicine and Fielding School of Public Health; and Gail Javitt, Director at Hyman, Phelps & McNamara.

Sponsored by
Partner Webinar

From June 2020

Olink Speakers: Ida Grundberg (CSO) and Erika Assarsson (Head of R&D).

You will learn:

  • About large-scale protein biomarker discovery studies for understanding of real-time human biology
  • How Olink high-multiplex immunoassay technology is combined with next-generation sequencing (NGS) readout
  • How 1,472 proteins can be measured with just 3 µL plasma/serum
Sponsored by
GenomeWebinar

Chief Medical Officer, Basilea Pharmaceutica International

President and CEO, GeneCentric Therapeutics

This webinar, Part 3 of the “Advances in RNA-based Biomarker Development for Precision Oncology” webinar series sponsored by GeneCentric Therapeutics, will discuss novel and emerging applications of RNA-based genomic analysis in precision oncology, form characterizing the tumor microenvironment to informing the development of immuno-oncology treatments.

Marc Engelhardt of Basilea Pharmaceutica International will discuss work showing that differential induction of gene expression may explain differences in reported adverse event profiles of targeted anticancer agents. His talk will detail the analysis of gene expression induction in safety relevant normal tissues from patient-derived xenograft models as an approach to rationalize and identify the molecular basis of adverse event profiles of targeted anticancer agents.

Michael Milburn, President and CEO of GeneCentric, will follow with a discussion of the utility of bulk tumor RNA-seq analysis in drug development. In particular, he will cover aspects of specimen and study design for bulk tumor genomics, as well as advantages and challenges of RNA-based diagnostics over DNA variations.  Development of immunogenomic analyses and GeneCentric’s overall technology approach will be highlighted.  This includes looking beyond RNA transcriptomics and utilizing RNA sequence data in drug development.

Sponsored by
GenomeWebinar

Boehringer-Ingelheim Endowed Professor of Internal Medicine,
Chief of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Yale School of Medicine

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease characterized by irreversible scarring of the distal lung, leading to respiratory failure. Currently, there is no cure for the disease and while studies have pointed to possible distinguishing molecular features, high-resolution cellular insights are still needed.

Harnessing technologies such as single-cell RNA-sequencing (scRNA-seq) may enable a better understanding of the cellular and molecular processes that determine the IPF lung phenotype, and lead to the identification of novel, cell type-specific therapies and biomarkers. 

In this webinar, Dr. Naftali Kaminski of Yale University will describe research that leveraged scRNA-seq to uncover the diversity and complexity of aberrant cellular populations in the IPF lung.

Dr. Naftali Kaminski will discuss details of the study and its findings, including:

  • Steps to generate a comprehensive IPF lung cell atlas from 312,928 cells collected from human IPF lungs, chronic obstructive pulmonary disease lungs, and control donor lungs
  • Identification of a previously undescribed aberrant basaloid cell type highly expressing genes implicated in the pathogenesis of IPF and marked by features characteristic of cells involved in distal airway development and repair
  • Resulting hypotheses on the relationships between the transcriptional profiles of cells identified in IPF lung tissues, function, localization in tissue, and disease pathophysiology
 
Sponsored by
Partner Webinar

Dirk Schacht obtained his Diploma in Biology, which was focused on microbiology and genetics, from the University of Kaiserslautern, Germany. Before joining Qiagen in 1998, he held various national and international sales and marketing positions in diagnostic companies. Dirk is currently Associate Director Global Product Management in Qiagen's PCR Systems & Assays Team.

Supplier efficiency adds an extra challenge to development of tailored components for your assays. Commercializing molecular assays requires a partner to provide quality components, supply security and capabilities for expansion.

Qiagen is a leading provider of PCR solutions with proven know-how in the development of molecular assays and reagents. We are also strong in optimizing production procedures. Through our experience as an OEM partner, we have created tailored solutions we offer in molecular kit and assay development. By partnering with us you don’t only get quality components and expertise, our vast portfolio breadth allows you to enhance your supply chain efficiencies.

In this on-demand webinar, Dirk Schacht describes Qiagen’s approach to kit development and respective support options for OEM partners around RT- and PCR-enzymes, mastermix formulations, assay development and their supply.

Sponsored by
Partner Webinar

Discover the latest advantages of using a personalized, tumor-informed circulating tumor DNA (ctDNA) test to design oncology clinical trials in solid tumors.  Learn how Signatera, a breakthrough technology, can be applied in early stage and late stage cancer trials, potentially enriching for patients most likely to respond to therapy, accelerating time to trial readout, or identifying early relapsers.  

Topics include:

  • Advantages of a personalized, tumor-informed ctDNA assay for molecular residual disease detection
  • Signatera clinical data in early and late stage solid tumors
  • Applications of Signatera in clinical trial design to maximize trial success, and accelerate time to data readout
Sponsored by

Pages

The Washington Post reports that US states and territories are seeking more funding for the distribution of SARS-CoV-2 vaccines.

The strain now accounts for about 80 percent of cases in Wales and Scotland, and about half of cases in England, the Guardian reports.

A new study suggests that using CRISPR to edit human embryonic DNA can lead to the loss of whole chromosomes, as the Associated Press reports.

In Science this week: ancient dog genomes highlight long ties with humans, genomic analysis of 40,000-year-old early East Asian individual, and more.

Interested in Posting your Webinar or White Paper on GenomeWeb?

Contact us