GenomeWebinars

Tue
Feb
26
1:00 pm2019
Sponsored by
Advanced Cell Diagnostics

A Cellular and Molecular Phenotyping Pipeline for Target Characterization in FFPE Biobank Samples

Genome Webinar

Associate Professor in the Department of Medicine, McMaster University 

Masters Candidate, McMaster University

This webinar will demonstrate how a research team at the Firestone Institute for Respiratory Health at McMaster University developed a cellular and molecular phenotyping pipeline using archived samples of lung tissue derived from patients diagnosed with fibrotic interstitial lung disease. 

Dr. Kjetil Ask will discuss how the clinically relevant tissues were obtained, clinically categorized and deidentified. He will provide his perspective on the requirement of cross-disciplinary expertise and the associated technological platform required for the identification and quantification of cellular and molecular targets in fibrotic lung disease. Dr. Ask will also discuss the potential application of this platform to pre-clinical models of lung disease. 

Megan Vierhout will present her research on the role of alternatively activated macrophages and endoplasmic reticulum stress in fibrotic lung disease. She will show specific examples of automated immunohistochemistry and associated in situ hybridization technology using ACD RNAScope and BaseScope assays to demonstrate molecular phenotyping and target identification. 

Sponsored by

Assistant Professor of Pharmacology in Medicine, Weill Cornell Medical College

Knowledge of the interactions between B-cells, T-cells, and follicular dendritic cells within germinal centers (GCs) is important for understanding the main determinant of GC B-cell fates. Given the very complex mixture of GC B-cells undergoing several different transitional states, single-cell transcriptional analysis is an effective way to precisely tackle how mutations occurring in GC-derived B-cell lymphomas affect these states and eventually cause cell transformation.

In this webinar, Dr. Wendy Béguelin of Weill Cornell Medicine will discuss how she used the BD Rhapsody single-cell RNA-seq platform and YFP floxed reporter mouse models to study how lymphoma-associated mutations disrupt the immune system by affecting GC B-cell states, explaining the biology of initiation of low-grade follicular lymphoma.

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

Instructor of Pathology, Medical College of Wisconsin

Outbreaks of influenza infections are seasonal and can range from regional outbreaks to nationwide epidemics or even global pandemics. Mortality can range from 4 percent to 60 percent for at-risk patient populations, depending on the strain circulating in the environment. Rapid diagnostics can significantly improve patient care and control outbreaks by treating with antivirals and informing patients of proper precautions to reduce spread.

Over the past decade, there has been a large shift in diagnostic options, moving from cell culture to rapid point-of-care testing. Today, multiple CLIA-waved assays are approved and laboratory managers must decide which methods and assays are appropriate for their healthcare environment.

In this webinar, Dr. Faron will discuss current trends in influenza epidemiology, evaluate current FDA-cleared assays, and present the MCW team's findings on a recent time-of-motion study comparing three rapid influenza assays. Overall, these data should aid healthcare providers to improve and implement rapid influenza testing.

Director of Research and Clinical Trials, Tricore Reference Laboratories

This webinar will discuss how a new multiplexed testing system can help physicians rapidly diagnose acute respiratory infections in the near-patient setting.

Acute respiratory tract infections are caused by a wide range of viral and bacterial pathogens and may share similar clinical presentations that make it difficult for physicians to diagnose based on symptoms alone. Syndromic testing with multiplex molecular panels offers clinical labs a way to quickly distinguish between a broad array of respiratory pathogens.

Join Dr. Steve Young of Tricore Reference Laboratories as he presents a new technology for multiplexed respiratory testing in acutely ill patients. He will share data demonstrating the capabilities of syndromic respiratory testing as well as his impressions on the ease of doing comprehensive syndromic testing using the QIAstat-Dx solution*.

*coming soon

Sponsored by

Professor of Bioinformatics, Microbiology and Cell Science Department, University of Florida

This webinar provides a comparison of next-generation sequencing (NGS) approaches for human transcriptome sequencing, including short-read Illumina sequencing and synthetic long-read sequencing technology.
 
NGS is a powerful method for characterizing eukaryotic gene expression. While short-read transcriptome sequencing data is inexpensive, it has major shortcomings, including difficulty detecting isoforms and gene fusions, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long-read sequencing such as PacBio Iso-Seq, meanwhile, offers long reads but at increased cost, higher error rates, and reduced quantification abilities.
 
Another approach, LoopSeq synthetic long-read sequencing technology from Loop Genomics, uses unique molecular identifiers to generate synthetic long reads on short-read Illumina sequencing instruments and no additional hardware. This method offers a promising option for human transcriptome sequencing by providing full-length mRNA sequencing coupled with UMI-based transcript counting for gene expression quantification.
 
In this webinar, Ana Conesa, Professor of Bioinformatics at the University of Florida, discusses a comparison study of short-read Illumina transcriptome sequencing and LoopSeq Transcriptome sequencing data for human transcriptome studies.

This is the second Loop Genomics GenomeWebinar on the topic of long-read versus short-read sequencing approaches. The first, which compared these methods in the context of microbiome sequencing, is available on demand here.

Sponsored by
Tue
Mar
26
11:00 am2019
Sponsored by
PerkinElmer

Advancing Agricultural Genomics with Low-Cost NGS Genotyping

Genome Webinar

Director and Founder, Texas A&M AgriLife Genomics and Bioinformatics Service

This webinar will address the current status and future directions for massively high-throughput genomics for plant and animal breeding and research.

A major drawback to sequencing-based agriculture studies has been the cost. Arrays and reduced representation sequencing methods are common alternatives for genotyping, but each of these methods has significant limitations associated with it.  

In this webinar, Charles Johnson, founder of the Texas A&M AgriLife Genomics and Bioinformatics Service, will share how his team developed a new approach, called AgSeq, to address these shortcomings.

AgSeq is a novel agriculture-focused genotyping pipeline that uses optimized laboratory processing, massive sample multiplexing, and machine learning to obtain highly accurate genotype information from low-coverage sequencing data. The reduced cost of whole-genome sequencing afforded by AgSeq allows for a substantial increase in individuals genotyped per study. AgSeq is powered by optimized library prep, automation, and high-throughput sequencing coupled with a reduction in the amount of data needed per individual. Data from individual samples is used to accurately impute gaps resulting from reduced coverage, allowing for accurate genotyping of large populations for plant and animal studies.  

Sponsored by
Wed
Mar
27
12:00 pm2019
Sponsored by
Swift Biosciences

How One NGS Core Lab Reduced Sequencing Costs with a Novel Library Normalization Kit

Genome Webinar

Senior NGS Specialist, UCL Genomics

Sequencing workflows require library quantification and normalization to ensure data quality and reduce cost. Traditionally, prior to sequencing, next-generation sequencing library technicians and automation strategies have had to undertake numerous steps to quantify and normalize NGS libraries.

In this webinar, Tony Brooks, Senior NGS Specialist at University College London Genomics, will discuss how his core facility implemented the Swift Normalase Kit, a novel enzymatic library normalization product that streamlines the cumbersome steps following NGS library preparation. 

Compared to conventional normalization, Swift Normalase saves sequencing costs by reducing read depth variation within a pool from a typical CV of 10-25% to a CV <10%. With a simple bead-free, quantification-free, two-step workflow, Normalase enables bulk processing of samples and expedites library pooling and loading to save time and cost.

Tony will share how his lab used the Swift Normalase kit for RNAseq library normalization to improve his facility's sequencing workflow and to reduce cost.

Sponsored by

Member of the Molecular Cardiogenetic Laboratory, Hospices Civils de Lyon, France

 

Clinical Application Product Manager, Sophia Genetics

This webinar will present the utility of a personalized in silico analytical approach for the routine clinical diagnosis of channelopathies and cardiomyopathies.

The advent of next-generation sequencing (NGS) has greatly improved the ability to rapidly assess many genes at the same time, but the analysis and interpretation of complex genomic variants still remains a challenge. In order for NGS to find use in routine diagnostics, clinical laboratories must be able to overcome this complexity and enable better outcomes for patients.

Dr. Alexandre Janin, member of the molecular cardiogenetic lab at Hospices Civils de Lyon in France, has solved this complexity and successfully characterized difficult variants by adopting the Sophia Platform. Dr. Janin will discuss how the platform:

  • Enables fast and comprehensive analysis;
  • Detects copy number variations quickly and efficiently;
  • Facilitates variant interpretation by sharing knowledge among members of the national network for Hereditary Cardiac Diseases (Cardiogen)

Dr. Janin will be joined by Dr. Audrey Coiffic, Clinical Application Product Manager at Sophia Genetics, who will discuss the most recent developments in targeted solutions for the advanced detection of inherited cardiac diseases.

Sponsored by
Thu
Apr
11
1:30 pm2019
Sponsored by
Bionano Genomics

The 'Dark Matter' of Cancer Genomics: Revealing Undetected Structural Variants in Leukemia

Genome Webinar

Director,
Penn State Institute for Personalized Medicine

Director of Scientific Affairs,
Bionano Genomics

This webinar will review a recent study that applied whole-genome sequencing and optical genome mapping to identify a large number of previously undetected somatic structural variants in leukemia samples. 

Genomic analysis has driven major advances in leukemia, where the spectrum of driver mutations provides a much more rigorous classification of disease subtypes, with a correspondingly more robust prognostic power, than previous histological characterization.

In this webinar, Dr. James Broach, Director of the Penn State Institute for Personalized Medicine, will discuss a study that indicates there are far more structural variants in leukemia than previously thought.

Dr. Broach and his team combined whole-genome sequencing and optical genome mapping to a number of adult and pediatric leukemia samples. The method identified 97 percent of the structural variants previously reported by karyotype analysis of these samples, as well as an additional fivefold more such somatic rearrangements. 

The method identified on average tens of previously unrecognizable inversions and duplications and hundreds of previously unrecognizable insertions and deletions. These structural variants affected a number of leukemia-associated genes as well as cancer driver genes not previously associated with leukemia and genes not previously associated with cancer. Analysis indicates that the status of several of the recurrently mutated genes identified in this study significantly affect survival of AML patients.

Dr. Broach will discuss the implications of the findings, which suggest that current genomic analysis methods fail to identify a majority of structural variants in leukemia samples — an omission that may hamper diagnostic and prognostic efforts.

Sponsored by
Recent GenomeWebinars

COO, Gradalis

This webinar provides a first-hand look at how Gradalis, a clinical-stage immunotherapy developer, is using an information management solution from L7 to streamline its research, clinical, and manufacturing operations. 

Precision medicine and new classes of immunotherapy treatments, including cell and gene therapies, require a new category of "companion informatics" that automate and synchronize complex manufacturing, quality management, and treatment processes. L7’s Enterprise Science Platform (ESP) is a scientific information management solution that connects people, processes, lab instrumentation, and bioprocess equipment to simplify and optimize biologics research, manufacturing, and treatment. 

This case study showcases L7's ESP’s implementation at Gradalis, where hand-written batch records with manual calculations and ad hoc oversight were initially used for production, analysis, and reporting. 

The webinar demonstrates ESP's capabilities, including end-to-end visibility, control, compliance, quality management, and automation of an organization’s workflow. ESP interfaces with common lab instruments, bioprocess equipment, and software systems, bringing inventory management, product testing, environmental monitoring, and other quality systems into a single platform. 

Sponsored by
Thu
Feb
14
12:00 pm2019
Sponsored by
Oxford Nanopore Technologies

Transcriptome of an Agricultural Pest Delineated by Oxford Nanopore RNA-Seq

Genome Webinar

PhD Candidate, Department of Human Genetics
McGill University, Canada

This webinar describes a project that applied Oxford Nanopore long-read RNA-seq to explore the transcriptional landscape of a damaging agricultural pest.

Anthony Bayega of McGill University discusses the study, which looked at the transcriptional dynamics that occur during early embryo development of the olive fruit fly (Bactrocera oleae), a key pest of cultivated olive trees that costs the olive fruits industry an estimated $200 million annually.

Anthony and colleagues combined absolute gene quantification using internal RNA spikes, full-length cDNA sequencing using Oxford Nanopore long-read RNA-seq, and high-resolution timescale experimentation for the study. They generated a de novo transcriptome assembly and identified 3,553 novel genes and a total of 79,810 transcripts.

Dr. Bayega discusses how he and his team also refined gene models for key sex-determining genes, which might provide insights into biological control of this fly.

Sponsored by

CEO, One Codex

This webinar provides a comparison of several next-generation sequencing (NGS) approaches — including short-read 16S, whole-genome sequencing (WGS), and synthetic long-read sequencing technology — for use in microbiome research studies.

NGS is a powerful method for characterizing complex microbial mixtures, but both short-read 16S and WGS methods have their shortcomings. While short-read 16S data is inexpensive, it only enables family- or genus-level identification, is not comparable across different variable regions, and provides poor relative abundance estimation. WGS, meanwhile, offers more accurate relative abundance estimation and greater specificity, but at increased cost and complexity.

Another approach, LoopSeq synthetic long-read sequencing technology from Loop Genomics, offers an intermediate solution by providing species-level identification and significantly improved relative abundance estimation over short-read 16S data. LoopSeq uses unique molecular identifiers to generate synthetic long reads on short-read Illumina sequencing instruments. 

In this webinar, Nick Greenfield of One Codex discusses a comparison study of short-read 16S, WGS, and LoopSeq data for four samples – two known composition-positive controls, including a 20-organism bacterial mixture from ATCC, and two complex microbiome samples.

He shares details from this comparison as well as demonstrate how to analyze these datasets on the One Codex software platform.

This webinar is the first Loop Genomics GenomeWebinar on the topic of long-read versus short-read sequencing approaches. Part 2 will provide a comparison of (NGS) approaches for human transcriptome sequencing, including short-read Illumina sequencing and synthetic long-read sequencing technology. Register Here - Part 2.

Sponsored by

Associate Professor, Pediatric Infectious Diseases
Cincinnati Children’s Hospital

This webinar discusses the use of shotgun metagenomics to identify children at risk of hospital-acquired infection.

Our speaker, David Haslam of Cincinnati Children's Hospital, details methods used to eradicate colonization with pathogenic organisms and hopefully prevent bloodstream infections. He also discusses how bacterial whole genome sequencing and shotgun metagenomics can be used to track and prevent transmission of hospital-acquired infections.

Dr. Haslam shares how this work fits within his lab's goal of identifying risk factors for invasive infection due to multidrug resistant bacteria. His team is applying next generation sequencing and metagenomic analysis to identify changes in the microbiome that correlate with risk for invasive infection and is currently developing this assay into a clinically actionable test.

Vice President, TRAD,
Rhythm Pharmaceuticals

Founder and Chief Science Officer,
Genomenon

Rhythm Pharmaceuticals and Genomenon will discuss their efforts to assemble a database of mutations associated with rare genetic disorders of obesity, and how this was optimized to facilitate a deep understanding of the variant landscape of melanocortin-4 receptor (MC4R)-pathway genes. This database may help identify MC4R-pathway deficient individuals who might benefit from future precision therapies.

WHY ATTEND? Developing an evidence-based view of the genetic contributors to human disease can help improve the diagnosis of rare disorders and drive important advances in precision drug development. Learn how Rhythm Pharmaceuticals partnered with Genomenon to inform their understanding of rare genetic disorders of obesity and help identify patients who might be appropriate for participation in clinical trials.

DETAILS: By indexing over 6 million full-text genomic articles using the Mastermind Genomic Search Engine, 120 genes and over 10,000 variants were identified as being associated with obesity in the medical literature. Each individual variant was interpreted using the evidence assembled through an automated technical process. This novel semi-automated approach to variant identification and annotation was accomplished via the Mastermind genomic database and vetted using American College of Medical Genetics and Genomics (ACMG) guidelines.

Join Alastair Garfield, PhD, Vice President, Translational Research & Development (TRAD) at Rhythm Pharmaceuticals and Dr. Mark Kiel, Founder and Chief Science Officer at Genomenon, as they share how a database of genes and variants associated with obesity was developed in less than 60 days, including scientific evidence complete with literature citations and ACMG interpretations for each mutation. The machine-learning driven process replaced several years of manual research of the scientific literature to find obesity-related mutations.

You will learn:

  • The importance of published genetic evidence in ensuring the success of a drug candidate
  • How to rapidly assemble a comprehensive biomarker database of this genetic evidence using data available in Mastermind
  • Why automated approaches are required for such disease-variant projects
Tue
Dec
4
11:00 am2018
Sponsored by
Sophia Genetics

Clinical-Grade Exome Analysis for Complex and Unsolved Case Investigations

Genome Webinar

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

Clinical Application Product Manager
Sophia Genetics

This webinar will discuss the use of clinical-grade exome analysis application in complex case investigations.

Dr. Pantelis Constantoulakis of Genotypos Science Labs will first discuss the utility of Clinical Exome Solution by Sophia Genetics in routine clinical research and diagnostics. He will also share details of the application’s efficacy in investigating complex and unsolved clinical cases. 

Next, Dr. Georgios Stamoulis of Sophia Genetics will introduce new features in Sophia DDM dedicated to prioritization and filtering strategies of variants detected with exome-size applications.

Sponsored by
Mon
Dec
3
1:00 pm2018
Sponsored by
Advanced Cell Diagnostics

Application of a Novel ISH Approach to Elucidate Splice Variants in Schizophrenia

Genome Webinar

National Institutes of Health Graduate Student Partnership Program

Senior Image Analysis Scientist,
ACD

This webinar will demonstrate how a research team at the National Institutes of Health evaluated a novel in situ hybridization approach and applied it to study splice variants related to schizophrenia.

The neurotrophic factor neuregulin-1, as well as its neuronal receptor ErbB4, are risk factors for schizophrenia. Distinct ErbB4 isoforms are generated by alternative splicing, and the levels of specific receptor isoforms are altered in postmortem brains of patients.

Because of these splice variants differ functionally, it is important to identify the cells that express distinct isoforms. However, traditional molecular analysis tools such as qRT-PCR and RNA sequencing require the disruption of dissected tissue to isolate RNA. To investigate in different cell types the relative amounts of the four ErbB4 variants in morphologically conserved brain tissue, the NIH team used the BaseScope in situ hybridization system with specific oligonucleotides targeting single exon/exon boundaries and fluorescence signal amplification.

This webinar will outline how the NIH researchers first determined the specificity and sensitivity of the BaseScope system and then used it to identify regional and cell-type specific expression of ErbB4 isoforms in the brain. The presentation will also explain how the NIH team quantified both the BaseScope and RNAscope assay signals using the freeware CellProfiler combined with an in-house analysis pipeline.

Sponsored by

Vice President, R&D Amyris

This webinar will discuss how Amyris, a biotechnology company that develops renewable products for a broad range of applications and industries, uses large-scale microbial engineering to support its manufacturing processes.

Organisms offer unparalleled molecular diversity that can be tapped into for a wide array of practical and commercial applications, but there are numerous challenges associated with realizing the full potential within this molecular diversity. Microbes can be engineered to produce many biological targets, but optimizing this process requires repeated iterations of the design-build-test-analyze microbial engineering cycle. The rate at which each phase of the cycle can be executed, as well as the magnitude of strain improvement obtained from each iteration, directly affect the overall development time — and cost — for any product.

Amyris scientists have developed advanced tools for strain engineering, high-throughput screening, analytics, and bioinformatics that accelerate microbial engineering by improving and reducing the number of cycle iterations needed. Central to these capabilities has been the availability of large volumes of low-cost, but high-quality synthetic DNA, which enables the efficient interrogation of a diverse set of hypotheses.

The presentation will cover:

  • How Amyris uses Twist DNA for large scale microbial engineering
  • The automated platforms that enable Amyris scientists to rapidly cycle through a data-driven strain improvement process
  • The role that Amyris biotechnology plays with commercial partners in diverse industries by providing a sustainable, cost-effective alternative to traditional manufacturing practices
Mon
Nov
5
11:00 am2018
Sponsored by
Sophia Genetics

Overcoming Challenges in Solid Tumor Testing with Advanced AI

Genome Webinar

Molecular Biologist, Dijon University Hospital

Clinical Application Product Manager
Sophia Genetics

With the Next Generation Sequencing (NGS), genome sequencing has been democratized over the last decades with the detection of genomic alterations.

This webinar will discuss the different steps taken by the CHU de Dijon to move from a non-NGS lab to an experienced NGS lab and how Sophia Genetics has successfully accompanied the lab to use different diagnostic molecular applications to address their clinical needs in a short turnaround time using Sophia artificial intelligence (AI).

In the first part of the webinar, Dr. Caroline Chapusot will cover the set-up program used to implement the Solid Tumor Solution by Sophia Genetics in the lab and the advantages of this solution over previous lab’s tests.

Then, Dr. Chapusot will discuss two specific clinical cases addressed using STS and Sophia DDM platform for the analysis and the interpretation of the data.

Finally, Dr. Chapusot will discuss the vision of the CHU de Dijon over the NGS applications used for clinical and research purposes and their impact on the reimbursement system.

In the last part of the webinar, Dr. Shirine Benhenda of Sophia Genetics will briefly introduce a solution that will soon be launched to detect gene fusions, beside SNVs, Indels, MSI and gene amplifications in FFPE samples from various solid tumors.

The Solid Tumor Solution by Sophia Genetics is a molecular application that bundles a capture-based target enrichment kit with the analytical power of Sophia AI with and full access to Sophia DDM platform. The application is designed to accurately characterize the complex mutational landscape of solid cancers associated with lung, colorectal, skin and brain cancers using FFPE samples.

Sponsored by
Wed
Oct
24
11:00 am2018
Sponsored by
Thermo Fisher Scientific

What's the Best Technology for Rare Allele Detection in Pathology Research?

Genome Webinar

Head, Laboratory for Diagnostic Genome Analysis, Department of Pathology;
Medical University of Graz

A variety of technology choices are emerging as potential solutions for the identification of mutations in formalin-fixed, paraffin-embedded tumor samples and cell-free DNA for liquid biopsy analysis.

In this on-demand webinar, Dr. Karl Kashofer, head of the diagnostic genome analysis laboratory at the Medical University of Graz, describes an evaluation of digital PCR and targeted next generation sequencing for potential use in biomarker discovery and monitoring of pathology research samples.

Dr. Kashofer details his laboratory’s learnings, including:

  • What should you consider when choosing technology for pathology investigations?
  • How should you handle data interpretation for rare allele detection in samples with large deletions?
  • How do you optimize sensitivity in FFPE and cfDNA samples?
  • What are the key differences observed in digital PCR, Ion AmpliSeq, Ion AmpliSeq HD, and Oncomine cfDNA assays?

For research use only. Not for use in diagnostic procedures. 

Sponsored by

CEO, Girihlet

This webinar will address a range of methods for optimizing small RNA library preparation.

Anitha Jayaprakash, co-founder of T-cell receptor sequencing firm Girihlet, will provide her perspectives on sequencing small RNAs and its utility in the study of various applications, including miRNA profiling in various systems and other small RNAs such as piRNAs in the germline.

Dr. Jayaprakash will discuss challenges and complications that can occur during small RNA-seq library prep and ways to avoid them. She will review the various steps in small RNA-seq library construction and discuss how protocol optimization can improve results and increase user friendliness. She will also discuss the 4N sequencing method, which uses randomized adapters to reduce the ligation bias associated with small RNA sequencing.

Sponsored by

Medical Director, Clinical Pathways, Dana-Farber Cancer Institute; Senior Physician, Thoracic Oncology Program, Dana-Farber Cancer Institute & Assistant Professor, Harvard Medical School

Business Development, Philips Oncology Informatics

This webinar will provide a first-hand look at how the Dana-Farber Cancer Center is adapting its oncology care strategy in light of the rapidly evolving molecular landscape.

With advances in the understanding of tumor biology and drug development, oncologists must now incorporate patient factors and preferences, tumor characteristics and genomics, and treatment toxicities and cost. In this struggle to keep pace with scientific evidence and provide best-practice care for patients, a new approach to cancer care pathways is needed. 

In this webinar, David Jackman from Dana-Farber will discuss how his team considers evidence, how clinicians make on- and off-pathway treatment decisions at the point of care, and how varying genomic alterations in a patient’s tumor can be married to a drive towards enhanced clinical quality and an appropriate reduction in variation of treatment decisions, while maintaining a granular and “personalized” view of each patient.

Dr. Jackman will also review how Dana-Farber uses analytics and real-world evidence alongside clinical experience and published evidence in a continuous-learning framework.