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GenomeWebinars

Tue
Apr
23
1:00 pm2019
Sponsored by
N-of-One

AMP/ACMG/CAP Cancer Sequence Variant Guidelines: A Two-Year Status Report

GenomeWebinar

Clinical Director, Molecular Tumor Board & Medical Director, Gastrointestinal Cancers, Inova Medical Group

Professor of Pediatrics and Professor of Clinical Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine

Chief Scientific Officer, N-of-One, a Qiagen Company

In 2016, the Association for Molecular Pathology (AMP), in partnership with the College of American Pathologists (CAP) and American College of Molecular Genetics (ACMG), launched a set of guidelines meant to set industry standards for reporting of molecular diagnostic test results in oncology, using a tier-based system and defined levels of evidence. Upon the release of these guidelines, several laboratories and molecular diagnostic decision-support companies incorporated them into their reporting to give pathologists and treating oncologists a more consistent report format that clearly conveys the level of importance and evidence for each variant, enabling them to provide the most relevant treatment options for oncology patients.

In this webinar, Dr. Timothy Cannon, Medical Director for Gastrointestinal Cancers at Inova Medical Group, Dr. Marilyn Li, Vice Chief of the Division of Genomic Diagnostics at Children’s Hospital of Philadelphia, and Dr. Sheryl Elkin, CSO of N-of-One, a Qiagen company, will discuss adoption of the guidelines in the field to date, what’s working, and any new challenges/opportunities that have come from the initial launch.

Attendees can expect to learn about some of the complexities that exist in incorporating the AMP guidelines into treatment strategies, as well as what might be on the horizon in industry standardization for levels of evidence. The webinar will conclude with an opportunity for audience Q&A.

Sponsored by

Head of the Genome Analysis Center, Head of Molecular Endocrinology; Helmholtz Center Munich

This webinar will provide a wide-ranging overview of the promise for metabolomics in studying human health and disease, as well as its potential for integration with other -omics disciplines.

Our speaker, Dr. Jerzy Adamski of the Helmholtz Center Munich, will review current approaches in targeted and non-targeted metabolomics, highlighting differences in methodology, coverage, advantages, and disadvantages of either approach. 

This webinar will put a special emphasis on the universal applications of broad targeted metabolomics assays, which have shown promise in delineating factors contributing to the clinical phenotype, including intrinsic and environment-related processes. Dr. Adamski will also touch upon the benefits of calculating metabolite sums and ratios along the most important metabolic pathways.

The acknowledgement of the importance of host-microbiota interaction warrants a look at how metabolomics can help this rather young research field move beyond associations between disease risk and microbial genetics, and towards a more thorough functional understanding of the involved processes. For this purpose, Dr. Adamski will highlight selected metabolic pathways that are known to be associated with gut microbiota and affect health via direct metabolic and immune-related effects.

Finally, Dr. Adamski will discuss how metabolomics can integrate with other -omics technologies, providing examples of how metabolomics has enhanced genome-wide association studies, among others.

Sponsored by

Bioinformatician, Roslin Institute, University of Edinburgh

This webinar will discuss novel long-read transcript sequencing (LRTseq) methods for transcriptome annotation that could increase the efficiency and accuracy of future sequencing projects.

LRTseq technologies, such as Pacific Biosciences’ Iso-Seq and Oxford Nanopore’s cDNA sequencing, have the power to provide rapid high-quality de novo transcriptome annotations. However, standard cDNA library preparation methods for LRTseq capture a significant amount of degraded RNA and are often overpopulated with highly expressed genes.

Degraded RNA reduces the efficiency of sequencing and introduces uncertainty with respect to predicted transcription start sites. Highly expressed genes can dominate LRTseq data, resulting in a loss of coverage for lower expressed genes. This typically results in missing genes and alternative transcripts in the final genome annotation.

In this webinar, Richard Kuo of the Roslin Institute will discuss how his team addressed RNA degradation by using Lexogen’s cap-specific TeloPrime method to prepare full-length cDNA libraries. To reduce overabundant genes, Kuo and colleagues experimented with two methods of cDNA normalization.

He will present his team’s results using these novel methods of cDNA preparation for Iso-Seq sequencing and will also cover some basics of LRTseq and analysis pipelines for Iso-Seq (from raw data to transcriptome annotation). 

Sponsored by

Assistant Professor, Department of Pediatrics; Scholar, Clinical Translational Science Center, University of New Mexico Health Sciences Center

This webinar will discuss the benefits of virus-specific target capture combined with next-generation sequencing (NGS) to identify viral infections and conduct comprehensive genomic and transcriptomic interrogation.

The high diversity of inter-virus genome types and intra-virus genomic heterogeneity, together with the complexity of sample types, make NGS-based clinical virology difficult, arduous, and expensive. A single method that is able to use nucleic acids that are of low quantity and poor quality to examine both DNA and RNA viruses from a mixed cell population that may include human, bacteria, and viruses would be ideal.  

To this end, our speaker, Darrell L. Dinwiddie of the University of New Mexico Health Sciences Center, will discuss a method his team has been evaluating that uses virus-specific target capture probe sets coupled with NGS. 

Dr. Dinwiddie will discuss how this method has demonstrated significant improvement in respiratory viral identification and genome coverage compared to unenriched NGS. His team has shown the ability to effectively capture and sequence viruses that may differ from the probes by as much as 10 percent to 15 percent. These methods have worked for viral sequencing from purified viral stocks, in vitro cell culture, and clinical samples.

This webinar will also address the broader implications of this work, including surveillance, epidemiologic studies, and public health planning.

For example, in two hospital outbreak studies, Dr. Dinwiddie and colleagues have shown that target capture and NGS enabled sensitive discrimination of the relatedness of respiratory syncytial virus and human parainfluenza virus 3 isolates obtained during the outbreak and provided evidence for source of transmission.

In addition, through multi-year retrospective and prospective NGS studies of respiratory viral infections at multiple pediatric hospitals, Dr. Dinwiddie and his team have been able to examine seasonal respiratory virus genomic variation, evolution, and distribution for several respiratory viruses. This includes evaluating the match of vaccine to circulating influenza virus strains and the correlation between virus strains and clinical severity of infections.  The recently developed Human Pan Viral sequencing methods by Illumina and Twist Biosciences will enable similar studies not only for respiratory viruses, but for all types of human viral pathogens across all sample types of interest. 

Sponsored by

Clinical Microbiologist,
Ikazia Hospital

This webinar will discuss the implementation of a rapid 24/7 PCR service in a small urban hospital setting.

Modern PCR technologies are changing the workflow of medical microbiology laboratories, making it possible to get molecular test results within an hour instead of days to weeks. Smaller and cheaper analyzers also make multiplex PCR techniques possible for smaller laboratories without a molecular department.

This webinar will illustrate the impact of new PCR technologies in the hospital setting. Our speaker, Michiel van Rijn, is a clinical microbiologist and head of the Department of Clinical Microbiology at the Ikazia Hospital in Rotterdam. Although the Ikazia hospital is one of the smaller hospitals in Rotterdam (360 beds), it has offered a "24/7" PCR service to its medical staff for 10 years, starting with molecular screening for methicillin-resistant Staphylococcus aureus in 2009. The hospital has expanded its portfolio in the last decade, and most recently rolled out multiplex syndromic testing in 2018.

In this webinar, Dr. van Rijn will speak about the implementation of a rapid 24/7 PCR service in his hospital and the effects of this service on patient outcomes and clinical decision making strategies. In particular, he will share his experiences with QIAstat-Dx syndromic testing and his expectation of further use of this technique in the future.

QIAstat-Dx is coming soon. Currently available as DiagCORE. DiagCORE is not available in all countries.

Sponsored by

Lead Specialist, Clinical Genomics, Melbourne Genomics Health Alliance

This webinar will discuss the implementation of an enterprise-wide clinical genomics platform that is shared across 10 hospitals and research organizations in the Australian State of Victoria.

Built and managed by the Melbourne Genomics Health Alliance, GenoVic supports an end-to-end workflow for genomic testing across multiple independent testing laboratories and hospitals.

In designing the system, the Alliance focused on standardizing the integration of multiple laboratories to a single system and facilitating secure sharing of high-quality genomic information. Following a rigorous qualification process, the Alliance selected best-in-class tools for integration into GenoVic, delivering a standardized, integrated, and interoperable system to meet both the clinical laboratory and patient needs for the Alliance member organizations. 

Join Dr. Natalie Thorne, Lead Specialist, Clinical Genomics, to learn how the Melbourne Genomics Health Alliance:

  • Created an infrastructure for scalable delivery and sharing of high-quality genomic information securely, efficiently, and sustainably
  • Advanced deployment of streamlined clinical interpretation of genomic variants by partnering with Agilent and Alissa Interpret to improve workflow management, curation, and traceability
  • Facilitated the fast and changing pace of genomics by designing a flexible, modular environment to evolve as needs change over time. 

Dr. Thorne will share key learnings from the project that molecular diagnostic laboratories can use to bring efficiency to their variant interpretation workflow through standardization and integration.

 

Due to the location of our speaker, this webinar will be pre-recorded. You may submit questions in advance of the webinar via the registration page.

Alissa Interpret is a USA Class 1 Exempt Medical Device, Europe CE IVD, Canada and Australia Class I IVD Device.

Sponsored by

Medical Oncologist, Johns Hopkins Kimmel Cancer Center

Director of the Institute of Laboratory Medicine, German Heart Center of the Technical University

This webinar will present recent evidence that demonstrates how incorporating circulating tumor DNA (ctDNA) assessments into real-world patient management can influence patient care decisions, alter radiographic interpretations, and impact clinical outcomes.

In particular, this webinar will discuss OncoBEAM a ctDNA testing method based on BEAMing (Beads, Emulsion, Amplification, Magnetics) technology developed at the Johns Hopkins University School of Medicine. OncoBEAM provides highly sensitive mutation analysis for the accurate and reliable detection of rare tumor-derived DNA present in the blood of patients with cancer.

In this webinar, Dr. Evan Lipson of Johns Hopkins will share his experience on the clinical utility of ctDNA measurements as an adjunct to radiographic imaging for monitoring disease activity in advanced melanoma patients undergoing treatment with targeted therapy or immune checkpoint inhibitors. These results have important implications for the clinical management of patients receiving immunotherapy and demonstrate the value of performing ctDNA testing for better resolution of tumor activity when performed alongside routine imaging and clinical assessments.

Next, Dr. Stefan Holdenrieder of the Technical University of Munich will examine the value of KRAS-mutant ctDNA as a highly specific marker for early response prediction and treatment monitoring of advanced pancreatic cancer patients receiving chemotherapy. The discussion will focus on the potential clinical benefit of monitoring changes in ctDNA levels in response to therapy, which appear more pronounced and rapid than changes in established protein biomarkers.

Sponsored by

Associate Professor, Biomedical Engineering, Yale University

Director, New Collaborations, Isoplexis

This webinar will discuss cutting-edge single-cell approaches to discover biomarkers that could elucidate the mechanism of a variety of autoimmune disorders as well as autoimmune and inflammatory reactions to immunotherapies.  

Many therapeutics seek to address a large growing need in autoimmune and central nervous system diseases. Additionally, despite their success in addressing major challenges in refractory blood cancers, current immunotherapeutic strategies are still hampered by autoimmune-like reactions and neurotoxicity-related events. Inflammatory responses from T-cells, monocytes, and other immune cells can have detrimental effects on patients in each of these areas, but it is challenging to understand the functional profile of these immune cells, and thus how to use this type of information to predict progression of autoimmune-like responses.

Our speaker, Dr. Rong Fan of Yale University, will discuss IsoPlexis’ advanced immune-based approaches in systemic lupus erythematosus and adverse events like cytokine release syndrome and neurotoxicity in cell therapy. He will describe the uses of single-cell functional proteomics in determining correlates and drivers of these adverse reactions, and how these biomarkers may be used in the future to improve therapeutic development and intervention.

In addition, Jon Chen of IsoPlexis will share a case study showing that monocyte polyfunction in multiple sclerosis tracks differential responses to treatments for early diagnosis and early intervention.

This webinar will be pre-recorded. You may submit questions in advance via the registration page.

Sponsored by
Wed
May
15
11:00 am2019
Sponsored by
Thermo Fisher Scientific

Discovery of Exon-Level CNVs in Daily Practice for Constitutional Genome Testing

GenomeWebinar

Team Leader, Intellectual Disability & Congenital Anomalies, Department of Human Genetics, Radboud University Medical Center

This webinar will discuss how Radboud University Medical Center’s Department of Human Genetics is using exon-level copy number variant (CNV) detection by microarray to assist its efforts in constitutional genome diagnostics. 

Nicole de Leeuw of Radboud University Medical Center will share how CytoScan XON, a high-sensitivity exon-level microarray, compares with CytoScan HD in constitutional cytogenomics, in both prenatal and postnatal samples from patients with congenital anomalies and/or neurodevelopmental delay.

This webinar will share data supporting the use of CytoScan XON to test multiple genes for intragenic CNVs in the human genome and will demonstrate how the CytoScan XON yields good array test results with DNA samples from a variety of tissues of origin.

For Research Use Only. Not For Use In Diagnostic Procedures.

Sponsored by
Thu
May
16
1:00 pm2019
Sponsored by
PerkinElmer

A Comprehensive Workflow for Soil Metagenomics Analysis Using Shotgun Sequencing

GenomeWebinar

Scientist, R&D Department, Illumina

This webinar will discuss a comprehensive end-to-end workflow for soil metagenomic shotgun sequencing that offers an unbiased alternative to amplicon-based approaches to assess the composition of culture-free microbial communities and predict functional profiles. 

The soil microbiome represents a highly diverse and complex microbial community that contributes to many aspects of human, animal and environmental health. Due to the biodiversity of soil microbial communities and the presence of various PCR and library preparation inhibitors, such as humic substances, unbiased extraction of high-quality DNA for NGS has been challenging for soil metagenomic studies.

This webinar will focus on the following topics:

  • Utility of shotgun sequencing using culture-free soil samples
  • Validated methodologies for gDNA extraction, library preparation, and sequencing
  • User-friendly analytical pipeline for taxonomic classification, alpha-diversity measurements, hierarchical clustering, and functional potential

Due to the location of our speaker, this webinar will be pre-recorded. You may submit questions in advance of the webinar via the registration page.

Sponsored by

Senior Specialist Biomedical Scientist, Frontier Pathology

Specialist Biomedical Scientist, Frontier Pathology

Specialist Biomedical Scientist, Frontier Pathology

This webinar will provide a first-hand look at how a hematology/oncology lab in the UK set up and validated three molecular assays for routine in-house use.

Speakers from the Royal Sussex County Hospital (RSCH) laboratory, operated under the Frontier Pathology NHS Partnership, will share their experience implementing two assays for suspected BCR-ABL1-negative myeloproliferative neoplasms.

The RSCH lab has spent the last several years repatriating historical send-away hemato-oncology assays for JAK2 V617F and CALR exon 9. During this webinar, RSCH scientists Munyoro Guvamatanga, Anna Tarasewicz, and Rebecca Lough will share their experiences bringing these assays in-house.

The JAK2 V617F mutation assay was the first to be repatriated in 2015 and is performed using the CE-IVD marked ipsogen JAK2 RGQ PCR kit. More recently, the lab began detecting CALR exon 9 mutations using the CE-IVD marked ipsogen CALR RGQ PCR kit. The assays are performed using gDNA extracted from whole blood samples and subsequent real-time qPCR on the QIAGEN Rotor Gene Q MDx 5Plex HRM platform.

This webinar will describe the experiences and challenges associated with the setup and validation/verification of the assays in the RSCH laboratory.

Sponsored by

R&D Manager, ID-Solutions

VP of Commercial Operations, Stilla Technologies

This webinar will outline the entire liquid biopsy workflow from cell-free DNA isolation to mutation detection by Crystal Digital PCR with the Naica System from Stilla Technologies.

Our speakers will focus on detecting EGFR, BRAF, NRAS, and KRAS mutations as well as pediatric and adult cerebral tumor classification panels.

Attendees of this webinar will:

  • Understand the liquid biopsy process for EGFR, BRAF, NRAS, and KRAS mutations;
  • Learn about the benefits of the Crystal Digital PCR platform in combination with research-use-only kits;
  • Hear why digital PCR is a particularly useful technique for the detection of mutations, therapeutic monitoring, and resistance appearance;
  • Learn about the different steps of the liquid biopsy workflow, from DNA isolation to DNA quantification and qualification and DNA genotyping, with dPCR multiplex kits
Sponsored by

Director of Genomics and Genome Informatics,
Scripps Research Translational Institute

This webinar will provide an overview of polygenic risk scores, which aggregate dozens of genetic variants that have been linked to disease risk in genome-wide association studies (GWAS) into a single score.

Recently there has been growing interest in polygenic risk scores for predicting disease risk, expanding on the value of large GWAS. Various efforts have begun to demonstrate the utility of polygenic risk profiling to identify groups of individuals who could benefit from the knowledge of their probabilistic susceptibility to disease.

This talk will review the evidence supporting the personal and clinical utility of polygenic risk profiling and how it can be transformative for clinical care as well as drug discovery.

More specifically this webinar will:

• Describe the polygenic basis for common diseases.

• Describe how polygenic risk scores are generated. What are the various strategies?

• The utility of polygenic risk scores from multiple perspectives.

• Discuss “Genotype First” as a framework for the ethical use of genetics.

Sponsored by

Bloomberg reports that the DNA-for-cash deal reported in Kentucky might be a more widespread scam.

St. Jude Children's Research Hospital scientists have treated infants with X-linked severe combined immunodeficiency using gene therapy in an early phase study.

St. Louis Public Radio reports that some African Americans are turning to DNA ancestry testing to help guide genealogical searches.

In Nature this week: a genomic analysis of the snailfish Pseudoliparis swirei, ancient DNA analysis gives insight into the introduction of farming to England, and more.