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Chief of the Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases at the National Institutes of Health

Bioinformatician, NIAID Collaborative Bioinformatics Resource (NCBR)/Leidos

VP Research for immunoSEQ Dx, Adaptive Biotechnologies

T cells are the adaptive immune system’s first responders to any virus, circulating in the blood to detect and quickly multiply to attack the virus, and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection. 

In this webinar we’ll discuss:

  • Information and early insights from Adaptive Biotechnologies’ open-access ImmuneCODE COVID-19 database
  • Demonstrate how high-throughput sequencing of the T-cell receptor beta repertoire may reveal SARS-CoV-2-specific clonotypes
  • Describe the epidemiology of COVID-19 in a cohort of patient samples from Northern Italy
  • Discuss the presence of public SARS-CoV-2-specific clonotypes in COVID-19 patient samples and controls
  • Analyze differences in the clonal distribution of SARS-CoV-2-specific T cell clonotypes according to different degrees of disease severity
  • Reveal changes in frequency (expansions vs. contractions) of SARS-CoV-2 clonotypes during evolution of the disease

For Research Use Only. Not for use in Diagnostic Procedures.

Sponsored by
Partner Webinar

Chief Medical Officer, Bionano Genomics

Clinical Associate Professor, Obstetrics & Gynecology, Maternal Fetal Medicine


Consultant Clinical Scientist
Director of GenQA

Non-invasive prenatal testing (NIPT) continues to expand globally to support maternal-fetal patient care. With a growing number of available assays and more labs offering testing, it is essential to have consistency in reporting and the ability to compare results and validate current or new methods.

This on-demand webinar features a panel of experts who provide key insights into the current needs in prenatal testing, the complexities of selecting an assay format and performing quality control, as well as other challenges that labs face when setting up and validating an NIPT assay.

The panelists bring a wealth of expertise and differing viewpoints in clinical laboratory practice, diagnosis of pregnancy complications, and new molecular methods for diagnosis and treatment of pregnancy anomalies and complications. 

Sponsored by
GenomeWebinar

Computational Biologist and Senior Director of the Data Sciences Platform, Institute Scientist, Broad Institute

The Broad Institute and Illumina have partnered to co-develop and improve upon genomic analysis pipelines, starting with integrating methods from Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) hardware-accelerated informatics platform into the Broad Institute’s GATK (Genomic Analysis ToolKit) Best Practices small variant pipeline, resulting in DRAGEN-GATK Best Practices.

In this webinar, Eric Banks of the Broad Institute will describe some of the issues the development team encountered as it investigated the differences between DRAGEN and GATK tools, highlighting the improvements to methods implemented in the new Best Practices pipeline.

He will also explain how the team assessed functional equivalency between the open source and licensed (hardware-accelerated) version of the pipeline, showing results between the two methods on the same source input.

Sponsored by
GenomeWebinar

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

NTRK fusions are oncogenic drivers in a variety of tumors. The Food and Drug Administration has recently approved the NTRK inhibitors larotrectinib and entrectinib for the treatment of pediatric and adult patients with NTRK fusion positive advanced solid tumors regardless of tumor histology.

In children, the incidence of NTRK fusions is high (more than 90 percent) in certain tumors, such as infantile fibrosarcoma, congenital mesoblastic nephroma, and secretory carcinoma; lower (between 5 percent and 26 percent) in other tumors such as pediatric papillary thyroid carcinomas and a subset of pediatric gliomas; and rarely seen in different acute leukemia.

In this webinar, Marilyn M. Li of the Children’s Hospital of Philadelphia will discuss a study of a large cohort of pediatric tumors using custom-designed DNA- and RNA-based next-generation sequencing panels. The team found that NTRK fusions are more common in pediatric tumors compared to adult tumors and involve a broader panel of fusion partners and a wider range of tumors than previously recognized.

The identification of these NTRK fusions is essential for precise tumor diagnosis and accurate tumor treatment. Therefore, it is crucial to include NTRK fusions as part of tumor genomic profiling for pediatric cancer patients to facilitate pediatric precision cancer care.

For Research Only. Not for use in diagnostics procedures.

Sponsored by
GenomeWebinar

Senior Research Associate,
Lawrence Berkeley National Laboratory

This webinar will discuss a streamlined library preparation method for next-generation sequencing (NGS) that improves quality control testing capability while reducing the total number of steps compared to conventional multiplexed library workflows.

NGS library preparation methods typically entail quality control testing at the end of the workflow, which can be laborious, particularly for high-throughput applications. The streamlined modification discussed in this webinar, Fluorescent Amplification for Next Generation Sequencing (FA-NGS), replaces PCR with real-time qPCR and SYBR Green to save time and implement single tube and single reagent QC.

FA-NGS enables in situ monitoring of library amplification and replaces the need for a separate quantification step of individual libraries. Additionally, FA-NGS allows for melting curve analysis as an intermediate library quality control step to aid in troubleshooting library failures prior to sequencing.

Attendees of this webinar will learn:

  • How to integrate qPCR and melting curve analysis into high-throughput NGS library preparation
  • Potential applications to various library workflows
Sponsored by
September 17, 2020
Sponsored by
Thermo Fisher Scientific

Clinical Diagnosis of Developmental Disorders with Chromosomal Microarrays

GenomeWebinar

Senior Director, Cytogenetics Laboratory,
Greenwood Genetic Center

The prevalence of developmental disability among US children aged 3 to 17 years increased between 2009 and 2017, with as many as 1 in 6 children in the US reported to have a developmental disability diagnosis. Developmental delay/intellectual disability (DD/ID) is frequently accompanied with one or more congenital anomalies or dysmorphic features. 

Chromosomal microarrays (CMA) are an established technology that has demonstrated great sensitivity and specificity for detecting genome-wide copy number variants (CNVs) and now represents a robust technical platform for both medical genetics research and clinical services. The American Academy of Neurology, the American College of Medical Genetics, and the International Collaboration for Clinical Genomics recommend CMAs as the first-line test to aid in the diagnostic evaluation of intellectual disability.

CMA is replacing traditional karyotype and FISH as the first-line genetic test due to its greater sensitivity, higher resolution, genome-wide capability, and greater diagnostic yield. The CytoScan Dx Assay is the first FDA-cleared chromosomal microarray test to aid in the identification of the underlying genetic cause of developmental delay, intellectual disability, congenital anomalies, or dysmorphic features in children.

Join Barb Dupont from Greenwood Genetic Center to: 

  • Learn about the importance of CMA postnatal assessments for developmental delay, intellectual disability, congenital anomalies, or dysmorphic features
  • Discover the advantages of using a higher-resolution CMA solution when compared to conventional techniques such as karyotyping and FISH
  • Understand how CMA results from CytoScan Dx Assay can be used in conjunction with other clinical and diagnostic findings by healthcare professionals
Sponsored by
GenomeWebinar

Technical Director,
Weck Laboratories

Product Manager, PCR and qPCR Reagents,
Agilent Technologies

Surveillance analysis of potentially pathogenic microbes found in shared public resources is an important component of research aimed at understanding, preparing for, and protecting communities from potential widespread infection and transmission of infectious diseases. For example, wastewater testing for SARS-CoV-2 has emerged as an efficient, cost-effective, and reliable method for assessing and estimating population infection levels. This approach may provide data to develop predictive modeling tools, enabling hospital and ICU occupancy trend analysis in the future. 

The fastest and most affordable method to date for quantitative viral detection is the quantitative reverse transcriptase PCR (qRT-PCR) assay. This webinar will discuss background, technique, reagents and instrumentation used in wastewater testing as it applies to SARS-CoV-2 research, as well as implications for analysis of other pathogens and infectious diseases.

Disclaimer: Agilent products are NOT approved for COVID-19 testing, diagnosis, treatment, or mitigation. Agilent has not validated a product to detect the novel coronavirus.

Sponsored by
GenomeWebinar

Professor of Cancer Genetics & Surgery, Institute of Cancer and Genomic Sciences
University of Birmingham

Senior Manager of Scientific Affairs,
Lexogen

Colorectal cancer is the third most frequently diagnosed cancer after lung and breast cancer and, unlike these agents, has relatively few stratified molecular targets for therapy due to the complex, heterogenous nature of the disease.

In this webinar, Andrew Beggs of the University of Birmingham will discuss a project that performed stratified analysis of patients as a pre-pilot for the 100,000 Genomes project. His team performed whole-genome sequencing on fresh samples and, as proof of principle, 3’ RNA-seq on matched formalin-fixed, paraffin-embedded samples.

Dr. Beggs will demonstrate that by combining WGS and RNA-seq, many interesting insights can be gained into the underlying disease processes in colorectal cancer, allowing identification of new targets for therapy and disease stratification.

Dr. Lukas Paul, Senior Manager of Scientific Affairs  will talk discuss the acceleration of gene expression profiling projects with the massive multiplexing of 3’ mRNA-Seq libraries.

Sponsored by
GenomeWebinar

Founder and Executive Partner, Opus Three

Senior Vice President, Clinical & Corporate Development, GeneCentric Therapeutics

This webinar, Part 2 of the “Advances in RNA-based Biomarker Development for Precision Oncology” webinar series sponsored by GeneCentric Therapeutics, will focus on the development of RNA-based companion diagnostics for oncology.

The path to developing a companion diagnostic (CDx) is becoming increasingly complex as available technologies and therapeutic advancements outpace regulatory standards and procedures. RNA-based approaches require heightened awareness and vigilance in combination with a well-defined and robust bioinformatics process. This webinar will cover the processof developing RNA-based predictive response signatures for cancer therapeutics; clinical and therapeutic implications for this approach; and the regulatory requirements, tools, and milestones necessary for successful advancement of an RNA-based CDx.

Felix Frueh, founder of regulatory consultancy Opus Three, will provide a deep dive into the regulatory considerations of developing RNA-based companion diagnostics. He will contrast the development of companion diagnostics with non-companion diagnostics and will illustrate key differences using a series of examples. Particular emphasis will be paid to potential future RNA-based companion diagnostics and currently marketed RNA-based diagnostics.

Joel Eisner of GeneCentric Therapeutics will follow with a clinical and bioinformatics perspective on the development of RNA-based predictive response signatures as companion diagnostics. His presentation will touch on the development of prototype response signatures using in silico analysis of public datasets, the curation of retrospective clinical data to further develop prototype predictive response signatures, and other points.

Sponsored by
GenomeWebinar

Science for Life Laboratory, KTH Royal Institute Technology

Recent advances in spatially resolved transcriptomics have greatly expanded the knowledge of complex multicellular biological systems. The importance of spatial context to infer deeper biological meaning is unquestionable, but technological constraints have historically limited broad adoption for various applications.

The field has quickly expanded in recent years, and several new technologies have been developed that aim to combine gene expression data with spatial information. The vast array of methodologies displays fundamental differences in their approach to obtain this information and, thus, demonstrate method-specific advantages and shortcomings. Nevertheless, the field of spatially resolved transcriptomics is accelerating in technological advancement, and the many biological analyses made possible by this advancement are just beginning to be fully explored.

In this webinar sponsored by 10x Genomics, Dr. Joakim Lundeberg of the KTH Royal Institute of Technology will present: 

  • A historical timeline of spatial gene expression methods
  • The current landscape of spatial transcriptomic methods as well as their strengths and weaknesses
  • Applications of spatial transcriptomics in a broad spectrum of research areas, including oncology, immunology, and neuroscience 
  • Future developments in spatially resolved transcriptomics and where the field is heading
Sponsored by
GenomeWebinar

Director, Colorado Center for Personalized Medicine in the School of Medicine University

This webinar will provide an overview of how the Colorado Center for Personalized Medicine (CCPM) at the University of Colorado implemented a preemptive pharmacogenomic screening program via a large-scale research biobank and a robust biocomputing system.

CCPM is a multi-institutional collaboration to link extensive patient data to ‘omics’ information and promote development of optimal prognostic and diagnostic tools for the clinical setting.

The CCPM Biobank is collecting DNA from upwards of 500,000 consenting participants under a CLIA/CAP-compliant model. To date, more than 145,000 patients receiving care in the University of Colorado’s health system have consented to participate, and genetic data generated from Illumina’s Multi-Ethnic Genotyping Array (MEGA) have already been generated on the first 30,000. Exome sequencing of 100,000 patients per year is now underway.

To integrate high-dimensionality data being generated on biospecimens with the data captured in CCPM’s data warehouse, a robust computing resource was established. With this infrastructure in place, CCPM developed a clinical pharmacogenomic initiative, which includes preemptive return of clinical results via CCPM’s research biobank, automated clinical decision support (CDS) tools, and development and implementation of proactive strategies to engage stakeholders.

Sponsored by
GenomeWebinar

Scientist II,
Ultragenyx Pharmaceutical

Applications Scientist, Advanced Cell Diagnostics

This webinar discusses the use of digital spatial profiling to test a gene therapy for a rare neurodevelopmental disease that causes severe seizures, global developmental delay, and limits a patient’s ability to communicate.

Maggie Wright of Ultragenyx Pharmaceutical outlines her team’s approach to testing a gene therapy in a mouse model.

She discusses how the mice were administered the gene therapy and using the RNAscope ISH assay, assessed the distribution of the gene therapy mRNA to determine treatment efficacy.

Sponsored by
GenomeWebinar

This webinar will address the utility of exome sequencing for neurodevelopmental disorders research and will provide details of a comparison study of two exome probe kits in this field of study.

The genetic etiologies of many neurodevelopmental disorders, including epilepsy and intellectual disability, have been mapped out, and custom panels are available to help in their identification. Existing panels, while sufficient in detecting all variant classes, can be challenging for streamlining the lab workflow and for keeping up with frequent content updates. 

In this webinar, Dr. Gaëtan Lesca of Lyon University Hospital will share the results of a comparison of Roche’s SeqCap EZ MedExome Probes with the company’s new KAPA HyperExome Probes in a range of patients with neurodevelopmental disorders.

Attendees of this webinar will:

  • Gain a better understanding of the genetic etiologies of neurodevelopmental disorders
  • Appreciate the limitations of current tools to evaluate neurodevelopmental disorders
  • Understand the differences between the performance of the KAPA HyperExome Probes and Roche’s previous whole-exome sequencing solution.

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

Over 70 percent of breast cancers are estrogen receptor positive and are treated with endocrine therapy. Of those, 40 percent also harbor mutations in the PIK3CA gene, and are targeted by the PI3K-alpha inhibitor alpelisib (Novartis' Piqray). However, intrinsic and adaptive drug resistance is the norm with these agents and mechanisms of resistance are still largely unknown in the clinic.

In this webinar, Guotai Xu of Memorial Sloan Kettering Cancer Center will discuss results of CRISPR/Cas9 screens that he has run which suggest endocrine therapy and PI3K-alpha inhibitor resistance occurs  and may provide a basis to develop resistance therapeutic strategies to prevent or revert this resistance. Dr. Xu will share details of work in this area that was published in Nature in January 2020.

Sponsored by
GenomeWebinar

Alzheimer’s disease is genetically complex with no meaningful therapies or pre-symptomatic disease diagnostics. Most of the genes implicated in Alzheimer’s disease do not have a known functional mutation, meaning there are no known molecular mechanisms to help understand disease etiology. 

In this webinar, Mark T. W. Ebbert of the Mayo Clinic will discuss his team’s work toward identifying functional structural mutations that drive disease in order to facilitate a meaningful therapy and pre-symptomatic disease diagnostic.  

Some of the genes and regions implicated in Alzheimer’s disease are genomically complex and cannot be resolved with short-read sequencing technologies. These regions include MAPT, CR1, and the histocompatibility complex (including the HLA genes). 

Dr. Ebbert will share how the Saphyr system from Bionano Genomics resolves full haplotypes for these complex Alzheimer’s disease regions, as well as regions directly involved in other diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Parkinson’s disease.

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The FDA and CDC call for a pause in administering Johnson & Johnson's SARS-CoV-2 vaccine while reports of rare blood clots are looked into, reports the Wall Street Journal.

According to the Associated Press, a Swiss program aims to shepherd long-term science projects and diplomacy.

CNN reports that two new studies suggest the B.1.1.7 SARS-CoV-2 variant may be more transmissible, but may not lead to more severe disease.

In PNAS this week: analysis of pathway affecting acute kidney injury, parental-specific allelic expression in horse placenta, and more.

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