Close Menu

GenomeWebinars

Wed
Oct
23
12:00 pm2019
Sponsored by
Swift Biosciences

Single-Cell Methylation Profiling of Pediatric Tumors via a Unique NGS-based Approach

GenomeWebinar

Research Specialist,
Perelman School of Medicine at the University of Pennsylvania

Assistant Professor, Department of Genetics,
University of Pennsylvania

Senior Product Manager
Swift Biosciences

This webinar will illustrate how single-cell methylation sequencing can be applied to gain significant insight into epigenetic heterogeneity in disease states, advancing cancer research discoveries. 

Our speaker, Jennifer Flournoy of Perelman School of Medicine at the University of Pennsylvania, will discuss a single-cell methylation approach from Swift Bioscience that her team is using to study pediatric leukemia and gliomas.

Swift's Accel-NGS Adaptase Module enables construction of next-generation sequencing libraries from bisulfite-converted, single-stranded DNA from single cells. This module is optimized to maximize the recovery of DNA containing uracil residues and low concentrations of AT-rich template. The resultant libraries consistently exhibit superior complexity with reduced composition bias to provide a more faithful representation of the methylome. This approach has demonstrated greater than 2-fold increase in read mapping rate as compared to other methods, significantly improving the data output per run while reducing the sample sequencing cost.

In this webinar, Jennifer Flournoy and her colleague Dr. Hao Wu will detail how they are using this single-cell methylation method to contribute to the generation of multi-omic human tumor atlases and to inform therapeutic approaches for pediatric cancers.

Sponsored by

Associate Laboratory Director,
Versiti (formerly Blood Center of Wisconsin)

This webinar will tell the story of Versiti’s journey in transforming genetic testing from a manual to a digitized process. It will include detail on how the organization succeeded, pain points along the way, a novel approach to variant assessment, and future plans for the program.

Versiti (formerly Blood Center of Wisconsin) specializes in a wide range of services, including esoteric diagnostic testing, such as immunology, hematology, oncology, and serology.

In this session, Dr. Valerie Trapp-Stamborski will cover:

  • Bringing genetic testing onto a technical platform for improved efficiency, analysis, and reporting.
  • The anatomy of a novel variant assessment tool that is used to classify and assess variants of uncertain significance.
  • The organization’s efforts around integrated reporting for improved diagnostic insights.
Sponsored by
Thu
Oct
31
11:00 am2019
Sponsored by
PerkinElmer

The Power of Automation for NGS Capture Enrichment: Uniformity and Speed

GenomeWebinar

Laboratory Director, Center for Applied Genomics,
Children's Hospital of Philadelphia

This webinar will provide an overview of how the Center for Applied Genomics at Children's Hospital of Philadelphia has optimized its next-generation sequencing (NGS) workflow using a combination of PerkinElmer's Sciclone automation technology and target capture chemistry from Twist Bioscience.

NGS library preparation has traditionally been a long process and lacked high throughput capabilities when performed manually. With Sciclone automation, the quality and speed of library preparation is drastically improved while simultaneously simplifying the workflow.

In this webinar, Dr. Renata Pellegrino of CHOP will share how her team has combined the Sciclone automated liquid handler with unique chemistry from Twist in order to scale projects without compromising high quality standards.

Sponsored by

Head R&D,
Institut für Hämatopathologie Hamburg

Molecular Biologist,
Institut für Hämatopathologie Hamburg

This webinar will provide a look at how the Institute of Hematopathology in Hamburg, Germany, is implementing complex genomic testing for lung cancer. 

Lung cancer has become a prime example of the success of molecularly stratified therapies. A steady increase of therapeutically relevant biomarkers has underlined the need for complex diagnostic assays like hybrid capture next-generation sequencing (HC-NGS) technology, which allows for simultaneous detection of single nucleotide variants, insertions/deletions, copy number variants, and translocations on limited biopsy material.

The resulting information on tumor genotype is extensive, however, and requires sophisticated bioinformatic tools and experienced molecular biologists to precisely distinguish relevant alterations with likely pathological outcome from artefacts or polymorphisms. Reliable software solutions are required to aid precise pathological reporting and provide information on the appropriate biomarker-guided therapies as well as relevant supporting studies.

In this webinar, Dr. Markus Falk and Dr. Daniela Stefanie Schmidt from the Institute of Hematopathology will outline a study they performed to evaluate the Roche Diagnostics AVENIO Tumor Tissue Analysis Kit, an HC-NGS assay that includes 77 genes for expanded tumor profiling, on 24 lung cancer samples with known genotype.

Drs. Falk and Schmidt will also discuss their use of Roche's NAVIFY Mutation Profiler software platform for pathological reporting. They will detail how they evaluated the platform for feasibility, accuracy, and the potential to save time in report generation.

Sponsored by

Associate Professor of Pathology & Director of Molecular Pathology and Diagnostics,
NYU Langone Medical Center

This webinar will discuss an approach that uses machine learning and epigenetic signatures to more effectively diagnose brain tumors.

New applications are emerging that use data-driven DNA methylation classifiers to vastly improve the accuracy of solid tumor classifications, especially for brain tumors and sarcoma. 

DNA methylation technology is becoming part of a new precision medicine paradigm for central nervous system tumor diagnostics that uses epigenetics as a more accurate tool than standard pathology to guide diagnostic decisions at the time of initial presentation.

In this webinar, Matija Snuderl of NYU Langone Medical Center will share details of his team's work developing and implementing DNA methylation-based classification of brain tumors in the clinical setting.

Sponsored by
Wed
Nov
6
10:00 am2019
Sponsored by
Agilent

Innovations in NGS and CGH for Preimplantation Genetic Testing

GenomeWebinar

Chair, Department of Human genetics & Professor of Molecular Cytogenetics and Genome Research at KU Leuven  

Molecular Geneticist, Genesis Genoma Lab; PhD Researcher, Department of Medical Genetics, National and Kapodistrian University of Athens, Greece

Product Manager, Reproductive Genetics, Agilent

This webinar will provide an overview of the latest advances in genomics technology for preimplantation genetic testing (PGT), with a focus on the advantages of next generation sequencing (NGS) and comparative genomic hybridization (CGH) for specific indications.

Our first speaker, Anastasios Mitrakos, a PhD researcher in the Department of Medical Genetics of the National and Kapodistrian University of Athens and a molecular geneticist at Genesis Genoma Lab, will discuss the advantages of microarrays in embryo screening. 

Our second speaker, Joris Vermeesch of Katholieke Universiteit Leuven, will provide an overview of haplarithmisis — simultaneous haplotyping and copy-number profiling of DNA samples — and discuss its importance for PGT. 

Agilent's Jessie Theuns will also discuss the company's CGH and NGS solutions for PGT and how they are being implemented in labs. 

Sponsored by
Thu
Nov
7
2:00 pm2019
Sponsored by
Beckman Coulter

Maximizing Productivity in Urinary Tract Infection Testing

GenomeWebinar

Head of Pathology Department, Quality Manager,
Sampurna Sodani Diagnostic Clinic

This webinar will discuss strategies for urinary tract infection (UTI) testing with the focus of detecting avoidable urine cultures.

UTIs are the most common infection leading to an antibiotic prescription after a physician’s visit. The appropriate use of antibiotics for patients that are correctly diagnosed with UTI will foster antimicrobial stewardship. The excessive use of antibiotics is one of the contributing factors to antibiotic-resistant bacteria, which have become a global public health concern.

Microbiology laboratories urgently need rapid screening methods for the detection of bacteria in urine samples, since several clinical studies have indicated that about two-thirds of these samples will not yield any bacteria or will yield insignificant growth when cultured.

Join Dr. Ranjana Hawaldar of Sampurna Sodani Diagnostic Clinic to:

  • Discuss how UTIs impact healthcare settings and laboratory workloads
  • Review current alternatives for UTI testing
  • Assess the relevant factors associated with urine culture candidate screening
  • Propose strategies to introduce a urine culture candidate screening process in the laboratory to avoid unnecessary urine cultures

P.A.C.E. credit is available for your participation.*

*Beckman Coulter Inc. is approved as a provider of continuing education programs in the clinical laboratory sciences by the ASCLS P.A.C.E.® Program. These credits are recognized by the State of California. Most programs also provide State of Florida credits (with valid license number). At this time, we cannot issue continuing education credits for those who provide healthcare (or work for an institution that provides healthcare) in Massachusetts or Vermont.

Sponsored by
Tue
Nov
12
11:00 am2019
Sponsored by
Sophia Genetics

A Multi-Gene Sequencing Approach for Hereditary Cancer Syndromes

GenomeWebinar

Laboratory Diagnostician,
Laboratory of Medical Genetics, St. Elizabeth Oncology Institute

This webinar will discuss a cancer center's hands-on experience with a targeted approach for clinical cases of hereditary cancers.

Next-generation sequencing (NGS) in routine genetic diagnostic practices offers a rapid and cost-effective analysis for identifying pathogenic variants associated with hereditary cancer syndromes. To date, the Laboratory of Medical Genetics at St. Elizabeth Oncology Institute in Bratislava has analyzed more than 2,500 families with suspected hereditary cancer syndromes using the NGS technology.

The adoption of NGS not only allows for the simultaneous analysis of multiple genes but also accelerates the turnaround time for high sample volumes. However multi-gene NGS applications also present new challenges, such as the management of big data, the accurate detection and classification of genetic variants.

In this webinar, Dr. Romana Valenčíková, Laboratory Diagnostician at St. Elizabeth Oncology Institute, will share her experience and describe:

  • An approach to detect hereditary cancers using the solution from Sophia Genetics
  • Benefits and challenges of using multi-gene NGS in complex clinical cases
  • How to identify pathogenic variants in unexpected genes not directly related to the disease
Sponsored by
Wed
Nov
13
1:00 pm2019
Sponsored by
Agena Bioscience

Targeted Detection of MET and NTRK Oncogenic Variants in Routine Molecular Analysis

GenomeWebinar

Professor of Tumor Pathology & Head of the Molecular Pathology Laboratory,
University Medical Center Essen, Germany

This webinar will discuss advances in detecting MET and NTRK variants in tumor samples, which holds significant potential for diagnostic and research applications.  

MET oncogenic variants leading to diverse exon 14 splicing alterations are emerging as a new predictive biomarker that would be sensitizing to MET-targeted tyrosine kinase inhibitors. The splice site DNA somatic variants result in RNA splicing-based skipping of MET exon 14, which supports targeted therapies.

Fusions in the NTRK1, NTRK2 and NTRK3 genes, which encode neurotrophin receptors TRKA, TRKB and TRKC, result in overexpressed kinase function, leading to oncogenesis in a wide variety of adult and pediatric solid tumors. Novel compounds have recently been developed that selectively inhibit TRK fusion proteins. As these alterations affect multiple histologies, detecting the presence of fusions across these genes greatly advances clinical cancer research.

In this webinar, Prof. Hans-Ulrich Schildhaus will present results from a study using a targeted, MALDI-TOF based method for the detection of MET exon 14 alterations and fusions across NTRK1, NTRK2 and NTRK3, and its applicability for routine screening.

Sponsored by

Director of Molecular Biology,
Mantis Diagnósticos Avançados

This webinar will discuss some of the issues laboratories face when transitioning to next-generation sequencing, and the key features to be considered for a successful implementation in routine testing.

Dr. Graziele Moraes Losso, director of the Molecular Biology division at Mantis Advanced Diagnostics Laboratory, will share the validation and comparison process her team used to help them smoothly migrate from real-time PCR and pyrosequencing to NGS testing. Dr. Losso will show some of her lab’s results working with somatic cancer testing using the GeneReader NGS System with different sample types (blood; formalin-fixed, paraffin-embedded; and liquid biopsies), and their performance in the European Molecular Genetics Quality Network (EMQN).

Dr. Losso will also discuss a case study with demonstrates the importance of having high quality NGS analysis and evidence-based interpretation when determining the actionability of test sample data.

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

Sponsored by
Mon
Nov
18
1:00 pm2019
Sponsored by
Mission Bio

Simultaneous Single-Cell DNA and Protein Sequencing in AML Samples

GenomeWebinar

Postdoctoral Research Fellow,
Memorial Sloan Kettering Cancer Center

This webinar will outline the results of a study that performed integrative single-cell genome and cell surface protein expression profiling of adult acute myeloid leukemia (AML) cases. 

Genomic studies of AML have identified mutations with varying allele frequencies, which suggests a step-wise acquisition of mutation in leukemogenesis. Bulk sequencing can provide prognostic information, but it cannot delineate clonal architecture at the single-cell level. Additionally, the complementation of immunophenotype with corresponding mutational analysis could elucidate important dynamics in the leukemic cell population, but has yet to be assayed in parallel.

In this webinar, Linde Miles of Memorial Sloan Kettering Cancer Center will share data from the study demonstrating that simultaneous single-cell sequencing of DNA and protein can identify populations of stem/progenitor cells with distinct clonal/mutational and protein expression profiles. She will also discuss how the method identified trends in protein expression when comparing multiple samples with similar mutations. 

Attendees of this webinar will learn about:

  • New DNA+protein capability from Mission Bio for simultaneous, targeted, single-cell DNA and protein sequencing
  • A novel 6-antibody cocktail in combination with a single-cell targeted DNA custom AML panel 
  • The relationship between mutational profile and cell surface protein expression in AML samples from six clinical research samples 
Sponsored by
Tue
Nov
19
11:00 am2019
Sponsored by
Stilla

Digital PCR for Tag Copy Number Assessment in CRISPR-Edited Cell Lines

GenomeWebinar

Research Technician, Jan Ellenberg Lab, European Molecular Biology Laboratory

Fluorescent proteins or self-labeling tags are invaluable tools for studying protein dynamics in living cells using fluorescence microscopy. However, quantitative imaging requires physiological levels of expression of the target protein of interest (POI), especially when stoichiometric interactions of the POI need to be investigated.

CRISPR has enabled researchers to tag virtually any target gene of interest, resulting in physiological levels of expression of the corresponding POI. However, the generation and selection of cellular clones bearing the correct edit — that is, the expected number of tagged alleles and an absence of extra integrations — requires quantitative assessment of the tag copy number.

This webinar will describe the use of dPCR as a quick method for quantitation of green fluorescent protein copy number in CRISPR-edited HeLa cells. The discussion will also include an introduction to dPCR working principles and post-acquisition data analysis methods.

Sponsored by
Tue
Nov
19
3:00 pm2019
Sponsored by
Illumina

eRD GWAS: Unlocking Gene Expression as a Tool for Trait Mapping in Crops

GenomeWebinar

Director, Plant Sciences Institute,
Professor, Department of Agronomy,
Iowa State University

This webinar will discuss eRD-GWAS, or "expression read depth genome-wide association study," a genome-wide approach for identifying genes whose expression patterns affect phenotypic traits.

To better understand the effect of gene expression on phenotypes, researchers at Iowa State University developed eRD-GWAS, a statistical method that identifies associations between variation in gene expression and variation in traits.

In this webinar, Iowa State's Patrick Schnable will share details of eRD-GWAS and discuss a study that used the approach in maize. 

After using RNA sequencing to assess transcription factor expression in five tissue types from 27 genetically distinct, inbred maize lines, Dr. Schnable and colleagues established an eRD-GWAS framework for assessing expression variation ties to phenotypic traits in a larger set of 369 inbred maize lines.

Dr. Schnable will share details of the study, which identified genes associated with 13 maize traits. He will also present a hypothesis that explains the high rates of true positive associations detected via eRD-GWAS.

Sponsored by

Pathologist,
Moffitt Cancer Center

This webinar will discuss how Moffitt Cancer Center has implemented a new capture-based application to accurately assess myeloid malignancies by detecting complex variants in challenging genes in a single experiment.   

Molecular profiling by next-generation sequencing (NGS) of myeloid tumors has become a routine part of disease management. One of the difficulties and limitations of NGS technology has historically been the inability to reliably detect mutations in certain GC-rich gene regions (such as the CEBPA gene) and insertions/deletions in genes such as FLT3, NPM1, and CALR. 

Many labs have circumvented these limitations by performing parallel orthogonal testing, which is redundant, costly, and inefficient.  Furthermore, in late 2018, the US Food and Drug Administration approved a targeted therapy for FLT3-mutated acute myeloid leukemia, making accurate and reproducible mutation detection of paramount importance for guiding treatment.

In this webinar, Dr. Mohammad Hussaini of the Moffitt Cancer Center will discuss development of a comprehensive solution that captures 98 genes noted to be of importance in myeloid disease. In particular, he will describe:   
  
- The process of evaluating and implementing this new capture-based NGS solution  

- The accurate detection of challenging genes such as FLT3, CALR, and CEBPA  

- The global analytical performance of this solution 

Sponsored by

Chief Technology Officer,
Karius

Genomics Bioinformaticist,
Amazon Web Services

The discovery of microbial cell-free DNA has propelled the introduction of new technologies that can be leveraged for next-generation diagnostic assays. Previously inaccessible genomic information can now be comprehensively surveyed for microorganisms, all from a single blood draw.

This webinar will outline how infectious disease testing firm Karius analyzes microbial cell-free DNA data through novel computational methods optimized for cloud scalability on AWS.

Sivan Bercovici of Karius will share how his team addresses the challenge of accuracy of genomic reference data, as well as the complexities that arise from the convoluted and highly homologous microbial signal. This capability offers the promise to fill gaps in current diagnostic methods, to empower physicians to more effectively detect and diagnose infectious disease, and to monitor the effectiveness of treatment.  

*This webinar will be pre-recorded.  You may submit questions for our speakers on the registration page.

Sponsored by
Mon
Dec
9
11:00 am2019
Sponsored by
Illumina

Emerging Biomarkers in Thyroid Cancer and NSCLC

GenomeWebinar

Associate Professor,
UCSD

This webinar will discuss emerging biomarkers for thyroid cancer and non-small cell lung cancer, with a particular focus on detecting gene fusions such as RET.

Our speaker, Dr. Sandip Patel of UCSD, will provide an overview of biomarker-guided therapies for thyroid cancer and NSCLC and will discuss key emerging biomarkers for these indications along with their supporting evidence.

Dr. Patel will also discuss different biomarker testing approaches, practical considerations, and address challenges around fusion detection.

The webinar will highlight hybrid-capture based comprehensive genomic profiling as a preferred method, along with a background and overview of this approach.

Sponsored by
Tue
Dec
10
11:00 am2019
Sponsored by
Congenica II

Maximizing Diagnostic Yield with an Optimized Variant Interpretation Platform

GenomeWebinar

Postdoctoral Researcher,
Royal College of Surgeons Ireland (RCSI)

This webinar will discuss the use of next-generation sequencing and an optimized variant interpretation workflow to increase diagnostic yield in complex clinical cases.

Using specific case examples as illustrations, Dr. Katherine Benson of the Royal College of Surgeons Ireland will discuss how her team has implemented an all-in-one solution for the analysis and interpretation of sequencing results in the epilepsy clinic. She will detail how this approach has increased diagnostic yield across all cohorts in a national epilepsy genomics project.

This webinar is a must-see for anyone working to optimize the diagnosis of complex clinical cases and improve patient outcomes in rare and inherited diseases.

In this webinar you will learn how to:

  • Increase efficiency of NGS data analysis and interpretation
  • Improve diagnostic yield in complex clinical cases
  • Provide faster, more accurate answers for patients
Sponsored by
Recent GenomeWebinars
Tue
Oct
22
1:00 pm2019
Sponsored by
Illumina

Genome to Phenome: A New USDA Blueprint for Animal Genome Research

GenomeWebinar

AAAS Science Policy Fellow,
US Department of Agriculture's National Institute of Food and Agriculture

This webinar will discuss a plan from the US Department of Agriculture to integrate animal genomics technologies into mainstream agricultural production strategies.  

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the “Blueprint for USDA Efforts in Agricultural Animal Genomics 2008–2017,” which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals required further research. In addition, new topics not covered in the original blueprint, which were the result of emerging technologies, required exploration.

To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled “Genome to Phenome: A USDA Blueprint for Improving Animal Production” in November 2017, and these discussions were used to develop new goals for the next decade. New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint.

In this webinar, Dr. Angelica Van Goor of USDA-NIFA will discuss details of the updated blueprint, which describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic.

Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.

Sponsored by
Mon
Oct
21
12:00 pm2019
Sponsored by
Agilent

Broad Genomic Testing for Oncology Clinical Trials and Clinical Practice

GenomeWebinar

Head of Medical Genomics,
Glasgow Precision Oncology Laboratory

Genomics is a key element in the potential of precision medicine to transform oncology. Hybrid-capture based targeted next-gen sequencing (NGS) represents a particularly promising option for cancer genomic testing, as it enables the profiling of all cancer-relevant events with the advantage of being compatible with formalin-fixed, paraffin-embedded (FFPE) tissue.

The Glasgow Precision Oncology Laboratory (GPOL) has defined the content required to capture the full range of clinically and biologically important genomic events that characterize solid tumors and turned these into a range of SureSelect cancer NGS assays, the first of which, dubbed Cancer Core, will be presented during this webinar.

In this webinar, Dr. Cooke, head of Medical Genomics of the GPOL shares:

  • How the GPOL has built affordable, fit-for-purpose, cancer NGS solutions using the SureSelect target enrichment platform, specifically to address the challenges of real-world oncology.
  • How the GPOL is implementing broad genomic testing as part of its mission to accelerate the translation of novel cancer therapeutics from discovery to clinical applications.

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

Sponsored by

Founder, President and Director, AdvaGenix

This webinar discusses best practices for designing an expanded carrier screening panel as well as interpreting large panels of genes.

Since the first carrier screening test for cystic fibrosis became available in the 1970s, the field has moved from biochemical testing to genetic testing. However, the cost of testing for a single gene is only marginally less than an expanded carrier test panel, which has made expanded carrier testing very popular. 

The challenge for offering expanded carrier testing remains the design of the panel as well as the interpretation of many detected variants. In this webinar, William Kearns, founder of genetic testing laboratory AdvaGenix, shares some strategies for designing a meaningful expanded carrier screening panel. He also discusses the Qiagen bioinformatics platform that AdvaGenix has implemented for interpreting large panels of genes.

Sponsored by
Tue
Oct
15
1:00 pm2019
Sponsored by
Agena Bioscience

PGx Beyond Drug-Metabolizing Enzymes: A Multigene Approach to Predicting Drug Response

GenomeWebinar

Lead Scientist,
University of Arizona Genetics Core for Clinical Services

This webinar will discuss a multigene approach to personalizing treatments for high blood pressure.

Although pharmacogenetic testing has become more widely adopted, providing patients with more genetically informed therapies, the vast majority of currently available clinical PGx testing focuses on genes involved in drug metabolism and transport. While these drug-metabolizing enzyme panels are important, there is evidence that in highly multifactorial diseases such as hypertension there are other genetic factors that strongly affect a patient’s response to therapies.

In this webinar, Dr. Ryan Sprissler of Geneticure will discuss a study examining these genetic determinants of hypertension therapy response that has shown that common and functional genetic variation plays a role in the variability of treatment effectiveness and may modulate the bell-curve response to many therapies.

Dr. Sprissler will share details on how these factors and subsequent trial data have led to the development of a multiplexed panel using a weighted algorithm to ultimately better predict individual therapy response.

Sponsored by
Thu
Oct
10
4:00 pm2019
Sponsored by
Roche

Laboratory Validation of a Kit-Based Liquid Biopsy NGS Assay

GenomeWebinar

Pathology Department and Cancer Research Division,
Peter MacCallum Cancer Centre, Melbourne, Australia

This webinar will provide an overview of how a pathology laboratory validated a 77-gene next-generation sequencing-based liquid biopsy assay.

Liquid biopsy provides a minimally invasive alternative to tissue biopsy for diagnosis, treatment selection, and monitoring of solid cancers. Liquid biopsy, especially the detection of molecular biomarkers from circulating tumor DNA (ctDNA), has evolved from single biomarker to multi-biomarker measurement with the application of NGS technologies, an advance that promises to improve clinical sensitivity — particularly for the detection of disease relapse and treatment resistance.

To date, the ctDNA-NGS space has been dominated by well resourced commercial providers offering accredited services based on laboratory developed tests. This webinar will describe how the Pathology Department at Australia's Peter MacCallum Cancer Centre is looking to bring this capability in house. Peter Mac's Andrew Fellowes will describe the analytical performance of the Avenio ctDNA Expanded Kit* in a cancer hospital pathology laboratory.

The Avenio ctDNA Expanded Kit* is a commercially available research use only kit based on Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) that promises to accelerate the uptake of liquid biopsy for clinical research of solid cancers in the clinical laboratory setting.

*For Research Use only, not for use in diagnostic procedures.

Sponsored by

Research Scientist, Center for Genomics of Neurodegenerative Disease, New York Genome Center

This webinar discusses a study that used spatial transcriptomics to gain insight into the molecular mechanisms of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease.

Mounting evidence indicates that dysfunction in signaling between motor neurons and glia is a key component of ALS, but limitations of traditional gene expression profiling technologies, such as low throughput or lack of spatial resolution, have so far stymied efforts to understand how this dysfunction participates in the onset and spread of ALS pathology in the spinal cord.

Our speaker, Silas Maniatis of the New York Genome Center, shares how his team sought to gain a spatially resolved view of disease-driven gene expression changes that order these events.

Dr. Maniatis discusses how the NYGC team and collaborators from the Flatiron Institute, SciLifeLab, and the Broad used spatial transcriptomics — which generates quantitative transcriptome-wide RNA sequencing data through the capture of polyadenylated RNA on arrays of spatially barcoded DNA capture probes — to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients.

The study resulted in a comprehensive spatiotemporal, transcriptome-wide gene expression dataset combining resolution, replication, and biological perturbation. Dr. Maniatis discusses data from the study as well as the broader potential of the work for future studies of central nervous system disorders.

Sponsored by
Mon
Oct
7
11:00 am2019
Sponsored by
Thermo Fisher Scientific

Future-Proofing a Genomics Core: Considerations When Adopting New NGS Technologies

GenomeWebinar

Manager, Tumor Profiling Unit, Institute for Cancer Research in London, UK 

This webinar provides an overview of the sequencing capabilities of the Tumor Profiling Unit at the Institute for Cancer Research in London, with a focus on the lab's strategy for bringing in new genomics technologies.

Improvements in next-generation sequencing technology have historically focused on speed and throughput, while the latest advances are focused on data quality and sensitivity of detection. Adopting new technologies that offer greater genomic insights will bring current genomic labs gracefully into 2020 and beyond.

In this webinar, Nik Matthews, manager of the ICR Tumor Profiling unit, shares insight into the current state of NGS technology and considerations to remain at the forefront of improvements in data quality.

 

Sponsored by
Wed
Sep
25
12:00 pm2019
Sponsored by
HalioDx

Biomarker Evaluation for CAR T-Cell Therapy: Impact on Drug Development

GenomeWebinar

Vice President of Translational Medicine
Kite, a Gilead Company

CAR T-cell therapy is an innovative form of immunotherapy that is finding increasing use for the management of blood cancers. While this approach has demonstrated impressive results for some patients, there are still challenges such as toxicity and difficulty in predicting which patients will respond.

The immune microenvironment is one of the factors that influences clinical outcomes, so identifying immune biomarkers is critical to maximizing the benefits of CAR T-cell therapy.

During this webinar, Adrian Bot, Vice President of Translational Medicine at Kite, a Gilead Company, explains how biomarker evaluation for CAR T-cell therapy can elucidate the mechanism of action and impact drug development.

This webinar also includes a brief overview of HalioDx's Immunogram platform and how it can provide meaningful and actionable data through biomarker testing.

Viewers of this webinar will learn:

  • How CAR T-cell therapy fights cancer cells and the associated mechanism of action.
  • Why evaluating immune biomarkers in CAR T-cells is crucial.
  • How biomarker evaluation can impact immunotherapy drug development.
Sponsored by

Postdoctoral Research Fellow,
Cancer Research UK Edinburgh Center,
MRC Institute of Genetics and Molecular Medicine

This webinar discusses a study that compared nine different transcriptomic analysis technologies with matched fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) cancer tissues.

Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability, and to what extent gene expression data from different platforms can be compared or integrated. In order to explore the feasibility of integrating gene expression data from different platforms, Dr. Arran K. Turnbull of the Cancer Research UK Edinburgh Center and colleagues explored nine technologies, which varied in resolution, cost, and RNA requirements.

The study used sequential tumor biopsies from 11 postmenopausal women with estrogen receptor positive breast cancer treated with three months of neoadjuvant anti-estrogen therapy. Half of each sample was snap frozen in liquid nitrogen and half was FFPE.

Transcriptomic analyses were performed using the Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder, and Qiagen UPX 3’.

 Dr. Turnbull details the study’s findings, which include: 

  • Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.
  • A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution, and RNA requirements to fit the user’s needs.
  • Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.
Sponsored by

Associate Professor, Genomic technologies & immuno-genomics, Radboud University Medical Center 

Director of Scientific Affairs,
Bionano Genomics

This webinar outline how a team at Radboud University Medical Center is assessing ultra-long read optical mapping on the Bionano Saphyr system to replace classical cytogenetics approaches in routine testing and for the discovery of novel structural variants with potential scientific, prognostic, or therapeutic value that are missed by standard approaches.

Structural variants (SVs) are an important source of genetic variation in the human genome and they are involved in multiple diseases, including cancer and developmental disorders. The short read lengths of next-generation sequencing pose a limitation for identification of structural variants, which means that in the diagnostic setting, comprehensive analysis of all structural aberrations in a given sample still requires a combination of techniques, such as copy number variant (CNV) microarrays, karyotyping, and fluorescence in situ hybridization.

The Bionano technology for whole-genome optical mapping offers an extremely long-read technology, providing unmatched sensitivity to detect structural variation, genome-wide, at low cost and at a variant allele fraction as low as 5 percent. Bionano’s de novo maps can resolve complex repetitive regions, identify CNVs, and elucidate genome-wide structural variation like balanced/unbalanced translocations, inversions, and indels with high sensitivity and precision.

In this webinar, Dr. Alexander Hoischen discusses a study to systematically compare the sensitivity and specificity of high-resolution optical mapping in 100 leukemia samples and 50 samples with known germline cytogenetic aberrations against the standard-of-care workflow, and discuss how optical mapping can facilitate the next major advancements in medical genetics. This presentation supports the view that the combination of classical approaches could be largely replaced by high-resolution optical mapping as implemented on the Bionano Genomics Saphyr system. 

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

Sponsored by
Tue
Sep
17
1:00 pm2019
Sponsored by
Horizon Discovery

A CRISPR/Cas9 Approach for Monogenic Blood-related Disorders

GenomeWebinar

Postdoctoral Researcher,
Max Delbrück Center for Molecular Medicine 

In this webinar, Ngoc-Tung Tran, Postdoctoral Researcher at the Max Delbrück Center for Molecular Medicine, will provide a general introduction of the CRISPR/Cas9 system. He will summarize the current approaches to enhanced homology-directed repair for precise gene editing. Regarding gene therapy applications, he will point out the differences between precise gene editing by CRISPR/Cas9 and gene delivery by viruses. He will also discuss the potential limitations of CRISPR/Cas9 for clinical applications as well as the current status of solving these limitations.

The webinar will include an example of gene correction using CRISPR/Cas9 in his lab. Specifically, he will discuss ELANE mutation correction in patient-derived hematopoietic stem cells, and the potential of this approach as a potential gene therapy for severe congenital neutropenia.

Sponsored by

Director, Molecular Diagnostics Lab; Professor Pathology; Chair of Molecular Diagnostics Division
Virginia Commonwealth University Health System

This webinar discusses a next-generation sequencing approach for detecting genomic mutations in hematologic maglignancies.

Join Dr. Andrea Ferreira-Gonzalez, Professor of Pathology and Chair of Molecular Diagnostics Division at Virginia Commonwealth University Health System, to learn about the role of genomic testing in hematology.

Dr. Ferreira-Gonzalez introduces the different hematological disease states, their biology, and driver mutations. She provides an overview and background about the role these mutations play in blood cancers and the steps taken for the validation and implementation of a clinical assay for hematological malignancies using RNA and DNA as detection methods for NGS.

Sponsored by
Thu
Aug
29
1:00 pm2019
Sponsored by
PerkinElmer

Biobanking at Scale to Support Precision Medicine

GenomeWebinar

Professor of Genetics, Rutgers University
COO, RUCDR Infinite Biologics, Human Genetics Institute of NJ

This webinar outlines how RUCDR Infinite Biologics, the world's largest university-based biorepository, has implemented workflows and processes to support precision medicine applications.

RUCDR Infinite Biologics, a unit of the Human Genetics Institute of New Jersey, has been perfecting the science of biobanking, bioprocessing, and analytics. In this webinar, Andrew Brooks introduces how RUCDR Infinite Biologics has created novel workflows to address precision medicine applications and presents an overview of these workflows, cutting edge analytical approaches, and robust biomaterial storage processes.  

With a focus on primary sample processing and new technological innovations allowing for efficient and cost-effective nucleic acid extraction, he describes how discovery processes are maximized, and precious biomaterial resources are protected for future analyses in both research and clinical applications.

Sponsored by
Wed
Aug
28
12:00 pm2019
Sponsored by
Horizon Discovery

Beyond Cas9: CRISPR Gene Editing with Alternative Nucleases

GenomeWebinar

Director of the Center for Advance Genome Engineering,
St. Jude Children’s Research Hospital

This webinar will provide an overview of alternatives to the popular Cas9 nuclease used in CRISPR gene editing.

Genome editing using the CRISPR-Cas9 platform enables precise genetic manipulations within complex genomes. Although wild-type Streptococcus pyogenes Cas9 (SpCas9) was the first detailed CRISPR platform, this widely used nuclease is still limited by the canonical 5’-NGG-3’ protospacer adjacent motif required for SpCas9 binding and cleavage.

In this webinar, Shondra Miller of St. Jude Children's Research Hospital will discuss the pros and cons of several Cas9 variants and orthologues and how these alternative nucleases can be applied to genome editing workflows.

Sponsored by
Thu
Aug
22
11:00 am2019
Sponsored by
BC Platforms

Biobanks and the Rise of Precision Medicine: Lessons from the Estonian Biobank

GenomeWebinar

Vice Director, Institute of Genomics, University of Tartu,
Head of the Estonian Biobank Science Center

This webinar discusses how the Estonian Biobank, a cohort of more than 165,000 participants, is addressing industry challenges with data management and collaboration in the transition to precision medicine.

The explosion of big data, together with rapidly developing technology, holds untapped potential for drug discovery and personalized healthcare studies. Accordingly, biobanks are emerging as an essential tool for discovery and clinical development, with their extensive datasets originating from diverse profiles of individuals and populations. However, the full power of this data is yet to be unlocked, due to both industry and academia grappling with challenges in managing, harmonizing, and integrating data and resources.

The following webinar discusses the ways to address and potentially solve such industry challenges, with insights from the Vice-Director of the Estonian Genome Center, Tonu Esko. The Estonian Biobank is one of the world’s leading resources for developing precision medicine applications, with its forward-looking laws, longitudinal digital health repositories, and availability of biological samples. Their work aims to promote the development of human genetics research, collecting information on health issues and genetics of the Estonian population, and implement genomic data in medical practice, with the aim to improve population health.

The discussion highlights the Estonian Biobank’s experience supporting precision medicine and operating as a data partner in BC Platforms’ global network, a secure environment for data reservoirs to display their data collections, while maintaining ownership and security, for pharmaceutical researchers who seek diverse patient cohorts for clinical research and drug development projects.

Sponsored by
Wed
Jul
31
11:00 am2019
Sponsored by
Thermo Fisher Scientific

Considerations and Impact of Implementing Targeted NGS in Myeloid Malignancies

GenomeWebinar

Head, Division of Genetics Department of Lab Medicine and Pathology,
Saint John Regional Hospital

This webinar provides a first-hand look at how a molecular laboratory validated and implemented a targeted next-generation sequencing-based myeloid assay to expedite the assessment of myeloid malignancies and assist in the understanding of myeloid cancers.

The most recent version of the World Health Organization classification system for myeloid neoplasms and acute leukemia, published in 2016, added a number of important biomarkers and genetic alterations for the assessment of myeloid malignancies. As the list of relevant molecular markers continues to grow and new targeted therapies are approved, traditional, single-gene approaches for analyzing myeloid malignancies have become laborious and time consuming. Next-generation sequencing has emerged as the optimal solution by enabling comprehensive assessment of all relevant molecular markers in a single NGS run.

In this webinar, Dr. Nancy Carson, Head of the Division of Genetics at the Saint John Regional Hospital, discusses her team’s experiences as one of the first labs in Canada to implement an NGS-based myeloid assay.

Dr. Carson discusses:

  • Unique considerations and applications of NGS in myeloid malignancies
  • Overview of her experience with with analytical validation and implementation of the assay
  • Impact of the implementation of the assay to date through case studies
  • Future directions
Sponsored by

Professor Genetics KU Leuven, Group Leader VIB, Leuven, Belgium

Postdoctoral Researcher, VIB-KU Leuven, Belgium

This webinar outlines a project that performs large-scale and integrative single-cell genome and transcriptome profiling of pediatric acute lymphoblastic leukemia (ALL) cases at diagnosis, during drug treatment, and in case of relapse.

ALL is the most common cancer in children and shows extensive genetic intra-tumoral heterogeneity. This heterogeneity may be the underlying reason for an incomplete response to treatment and for the development of relapse.

Data from this study provides information about the sensitivity of each leukemia clone to therapy and about how relapse can develop. Moreover, the results point toward the feasibility to detect minor clinically relevant leukemia clones at diagnosis or during early days of treatment in ALL.

The main focus of this webinar is:

  • Introduction of the Tapestri Platform from Mission Bio for targeted single-cell DNA sequencing
  • Presentation of a novel custom panel covering the 300 most mutated genomic regions in ALL
  • Insights into the clonal architecture of pediatric T-ALL, lessons learned from the first 16 samples processed with this custom ALL panel
Sponsored by

Director of Fetal Medicine,
Harris Birthright Research Center for Fetal Medicine,
King's College Hospital

This webinar discusses the evolution of fetal aneuploidy screening and the most recent evidence around the implementation of prenatal cell-free DNA testing in clinical practice.

Non-invasive prenatal testing (NIPT) by cell-free DNA testing has rapidly become an integral part of clinical care, and clinical studies demonstrating its high accuracy for trisomy 21 are familiar to most obstetric providers.

In this webinar, Kypros Nicolaides, Professor and Director of Fetal Medicine at King’s College, London, reviews the most recent evidence demonstrating the clinical value of cell-free DNA testing in prenatal care, discuss different implementation models, and share his own experience with cell-free DNA testing for fetal aneuploidy. He also discusses the patient perspective and how different factors may influence the choices and preferences of pregnant women for prenatal care.

Sponsored by

Director of the Molecular Microbiology Laboratory; Associate Director of the Clinical Microbiology Laboratory, University of California, San Diego

Director of Molecular Diagnostics & Assistant Director of Infectious Disease Diagnostics, Northwell Health Laboratories; Director of Microbiology, Long Island Jewish Medical Center

This webinar shares the results of comparisons of commercially available nucleic acid amplification tests for use in routine screening of pregnant women for Group B Streptococcus (GBS).

GBS colonization occurs in about 18 percent of pregnant women worldwide and about 25 percent of pregnant women in the United States. Spread of GBS to newborn children occurs at an estimated rate of 40 percent to 73 percent, with about 1 percent to 2 percent of colonized newborns developing early-onset disease (EOD), which can include symptoms of septicemia, meningitis, or pneumonia, and may result in long-term disabilities such as retardation, hearing or vision loss, and potentially death.

The Centers for Disease Control and Prevention recommends universal screening with enriched culture-based methods at 35 to 37 weeks of pregnancy to identify women colonized with GBS. Nevertheless, EOD due to GBS still occurs, and 81 percent of neonates who develop EOD are born from mothers with a negative GBS screening test, suggesting a high rate of false negatives for culture-based screening tests. Therefore, screening methods are shifting to rapid and highly sensitive nucleic acid amplification tests (NAATs).

In this webinar, directors of two leading microbiology labs share studies that compared four commercial molecular GBS assays to the standard-of-care culture method.

Our speakers discuss how these assays compared to the standard of care as well as to each other.

Sponsored by
Tue
Jul
23
1:00 pm2019
Sponsored by
Qiagen: Nov 16, 2014

A Novel Quality Improvement Model to Support Molecular Testing of Oncology Patients

GenomeWebinar
Dr. Yaolin Zhou discusses Quality Improvement Model to Support Molecular Testing of Oncology Patients

Director of Molecular Pathology,
University of Oklahoma Health Sciences Center (OUHSC)

This webinar discusses how the Molecular Pathology Laboratory at the University of Oklahoma (OUMP) is using a new quality improvement model to support molecular testing of oncology patients. 

The oncology landscape is rapidly evolving due to new biomarker discoveries and targeted treatments. Biomarker testing is ideally performed in on-site molecular diagnostic laboratories to facilitate local communication and promote multidisciplinary collaboration.

However, assay implementation and incorporation is complex and full of potential pitfalls. Due to the costs and challenges associated with offering new molecular tests, labs need to take additional steps to ensure that the healthcare provided is effective, efficient, patient-centered, safe, and timely.

In this webinar, OUMP's Yaolin Zhou discusses how her lab approaches molecular testing as a quality improvement initiative. She presents the EPIDEM model of quality improvement, which stands for Exploration, Promotion, Implementation, Documentation, Evaluation, and Modification.

Dr. Zhou reviews specific applications of the EPIDEM model to improve molecular testing of leukemia, breast cancer, and melanoma patients and will also share OUMP’s approach to next generation sequencing using Qiagen's GeneReader NGS System.

Sponsored by
Thu
Jul
18
2:00 pm2019
Sponsored by
Thermo Fisher Scientific

Laboratory Stewardship: Improving Healthcare Delivery Amid a Changing Clinical Lab Environment

GenomeWebinar

Senior Healthcare Consultant,
ARUP Laboratories

This webinar explores the concept of laboratory stewardship as a way of viewing and improving healthcare delivery, through the consistent and persistent search for ways to increase testing efficiency and effectiveness, decrease waste, and therefore improve patient care quality. 

The old model for clinical laboratory testing focused largely on a fee-for-service reimbursement environment, where additional volume always translated to additional revenue, and tests were relatively inexpensive. Many laboratorians exerted little influence on provider test utilization practices and opted to simply perform whatever tests the provider ordered, whenever they were ordered. As a result, and not surprisingly, patterns of overutilization, underutilization, and mis-utilization of tests emerged and persisted.

This presentation supports a new model of laboratory service delivery, where laboratory leaders assume new roles of greater involvement and influence in the selection and performance of tests, as part of a collaborative team effort that crosses departmental boundaries. This concept and process has been referred to in recent literature as “laboratory stewardship” and has been the basis for significant patient care improvements in many laboratories. It fits perfectly within the new environment of accountable care organizations, rapid growth of expensive genetic tests, and the ongoing desperate attempts to control healthcare costs. It also fits well with efforts to improve lab testing efficiency and productivity, through the careful selection of QC materials and testing platforms.

This webinar demonstrates, through example and case study, several ways most laboratories, organizations, and patients can benefit greatly from the laboratory stewardship approach. It will emphasize the need to adopt a collaborative proactive approach to healthcare delivery, recognizing that the clinical laboratory is positioned uniquely to exercise considerable positive influence to this effort.

Learning Objectives:

  • Understand and be prepared to incorporate the concept of laboratory stewardship as a tool for improving patient care.
  • Review and discuss examples and case studies where stewardship interventions have resulted in significant savings and patient care improvements.
  • Go forward with a commitment to find and act upon stewardship opportunities in your own organization.
Sponsored by
Wed
Jul
17
1:00 pm2019
Sponsored by
GenomeWeb/ABRF

Expert Tips on Running a Mass Spec Core Lab Amid Rapid Technological Change

GenomeWebinar

Chief Scientific Officer,
Proteomic and Genomic Sciences

Assistant Professor and the Director of the Mass Spectrometry Core,
Buck Institute for Research on Aging

Manager, Proteomics Core,
UC Davis Genome Center

In this webinar, three experts share advice on how to efficiently manage a mass spectrometry core lab while staying ahead of the technology curve.

Our first speaker, Benjamin Orsburn of Proteomic and Genomic Sciences, discusses how core lab managers can balance efficiency and quality while keeping up with advances in mass spectrometry. As groundbreaking new techniques bring customers flocking to core labs with high expectations, the goalpost for maintaining “quality” can appear to be constantly moving. Dr. Orsburn describes extreme examples of core lab management principles that can help make time for R&D to add new lab techniques.   

Our second speaker, Birgit Schilling of the Buck Institute for Research on Aging,  discusses how her lab uses data-independent acquisition (DIA) workflows for a variety of collaborative projects, including small studies and larger scale projects. Dr. Schilling shares the criteria her team uses to decide whether to use published spectral libraries or to apply data-dependent acquisitions (DDA) to build their own spectral libraries that are used later to process the quantitative DIA data sets. Dr. Schilling also discusses the adoption of new technologies and the dissemination of data sets to collaborators and core users.

Our third speaker, Brett Phinney of the UC Davis Genome Center, shares how his team is developing efficient and more universal methods for the core lab. Researchers today expect core facilities to quantify thousands of proteins and their post-translational modifications efficiently and for a reasonable cost. This is generally feasible when there are a limited number of sample types and organisms, but when every sample has the potential to be different, it is difficult to develop methods that can apply to a wide variety of samples. Dr. Phinney details how his team uses suspension trapping and peptide-centric DIA in combination with deep learning to address this issue for both proteomic sample preparation and proteomic LC-MS/MS analysis.

More information on other webinars in this series can be found here.

Sponsored by
Mon
Jul
15
11:00 am2019
Sponsored by
GenomeWeb/ABRF

Proteomics for Precision Medicine: New Workflows to Support Translational Research

GenomeWebinar

Senior Director,
Thermo Fisher Precision Science Center

Head of Applications,
Evosep

This webinar addresses new translational workflows to support proteomic profiling for biomarker discovery through precision medicine.

Recent advances in mass spectrometry have expanded the opportunities for translational proteomics, which complements other omics disciplines such as genomics, transcriptomics, and metabolomics/lipidomics. However, a key challenge is bridging the gap between early-stage discovery and next-stage, routine quantitative application of biomarker assays in the clinical research setting.

To accelerate the discovery of clinically actionable biomarkers, workflow solutions need to address scalability, reproducibility, and robustness. They also need to support the analysis of larger patient cohorts.

Our first speaker, Emily Chen, senior director of the Thermo Fisher Precision Science Center, discusses the need to achieve precision proteomics as a first step toward achieving precision medicine. She presents precision medicine workflows that focus on biofluids and FFPE tissues and applications using these workflows.

Our second speaker, Nicolai Bache, head of applications at Evosep, discusses a new low-flow separation system for proteomics-based translational research.

More information on other webinars in this series can be found here.

Sponsored by
Tue
Jul
9
1:00 pm2019
Sponsored by
GenomeWeb/ABRF

Overview and Insights from the 2018/19 ABRF Multi-Laboratory DIA Study

GenomeWebinar

National Institute of Standards and Technology

Leibniz Institute on Aging – Fritz Lipmann Institute

This webinar outlines a project led by the Association for Biomolecular Resource Facilities to help academic and core facilities who are using Data-Independent Acquisition (DIA) technology for protein quantification.

Proteomics researchers are realizing the promise of DIA, but due to the variety of acquisition methods, there is a need to develop best practices and offer opportunity for adoption. The ABRF Proteomics Research Group (PRG) realized that there was a need for a go-to resource for new users interested in DIA studies. Such a resource would provide information about sample processing, data acquisition, and data analysis.

As part of this study, a prototype sample set was used that was comprised of a HeLa digest spiked with four non-human proteins at different concentrations. Upon request, this sample was provided to 64 participants from labs all across the world, along with recommended data-acquisition methods. Raw data was requested from participants for the PRG to analyze. The user profile of the 45 laboratories who submitted the data had a good representation of users who were new to DIA; as well as those who had prior DIA experience.

Results from this study and future plans will be presented in the webinar.

More information on other webinars in this series can be found here.

Sponsored by

Assistant Investigator, Stowers Institute for Medical Research

This webinar outlines a study that combined genome-wide and classical molecular approaches to demonstrate that translation strongly affects mRNA stability in a codon-dependent manner, ultimately influencing mRNA and protein levels in higher organisms.

Ribosomes are the most abundant RNA-binding structures in the cell, and while their main function is to decode nucleotides into amino acid sequences, translation can also affect mRNA stability depending on codon composition. This regulatory pathway is different from codon usage or bias and is known as "codon optimality," defined as the property of given codons to regulate mRNA stability in a translation-dependent manner.

In this webinar, Ariel Bazzini of the Stowers Institute for Medical Research details a study that took three independent approaches in different human cells. The team measured the decay of existing mRNAs by performing time-course RNA-seq; measured mRNA stability independent of untranslated regions (UTRs) using a vector-based library termed ORFome; and measured mRNA stability without blocking mRNA transcription using a method called SLAM-seq.

Dr. Bazzini discusses the study's findings, which provide valuable insights into a novel and powerful regulatory pathway that may be an underlying cause of misregulated gene expression in human conditions and diseases.

Sponsored by

Associate Professor, Pathology & Immunology; Section Head, Hematopathology;
Washington University School of Medicine in St. Louis

Global Product Manager, Genomics and Diagnostics Group,
Agilent Technologies

This webinar focuses on measurable residual disease (MRD) monitoring in post allogeneic hematopoietic cell transplantation (alloHCT) myelodysplastic syndrome (MDS) cases. 

Standard sequencing-based technologies have a limited ability to detect low-abundance mutations due to the inherit error rate of the sequencing technology and pre-analytic errors associated with PCR amplification and sequencing library construction. This approach is generally limited to the detection of mutations with variant allele frequencies (VAFs) of greater than 2.5 percent. 

Our speaker, Eric Duncavage, discusses an approach his team used to address this issue, which used HaloPlex HS error-corrected sequencing coupled with high-coverage depths that allowed them to detect VAFs as low as 0.03%, or one tumor cell in ~1,600 cells. 

Dr. Duncavage’s team applied HaloPlex HS to bone marrows collected prior to and 30 days after transplant in 86 MDS patients by targeting previously identified somatic mutations. They found that 32 of 86 cases (37 percent) had at least one mutation at day 30 post-alloHCT with a maximum mutation VAF greater than 0.5 percent (equivalent to 1 mutant cell in 100 cells).

Dr. Duncavage details the study, which found that cases who progressed had a higher maximum mutation VAF 30 days after transplant compared to those who did not. Multivariate analysis confirmed that the detection of a mutation with a VAF greater than 0.5 percent 30 days after alloHCT was associated with an increased risk of progression and decreased progression-free survival. 

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

Sponsored by
Thu
Jun
20
11:00 am2019
Sponsored by
Sophia Genetics

From Manual to Automated Library Prep: Implementation and Analytical Validation

GenomeWebinar

Molecular Geneticist,
Medical Genetics Laboratory of Ospedale Pediatrico Bambin Gesù

This webinar will discuss how a clinical lab rapidly implemented a robust automated library preparation workflow that reduces hands-on time and increases sample throughput for a better diagnosis of kidney diseases.

The adoption of next-generation sequencing (NGS) in clinical laboratories has drastically changed the way genomic analyses are performed. With its ability to deliver comprehensive target coverage, NGS technology enables the detection of low-frequency variants and accelerates turnaround times for high sample volumes. But despite the vast improvements in sequencing methods that have decreased bias rates, data analysis can still be impaired by human errors during library preparation. Considering the complexity of the workflow and the elevated number of samples, library preparation remains a time-consuming and resource-intensive process, leaving many laboratories at increased risk of human error.

In this webinar, Dr. Dario Cocciadiferro, molecular geneticist at the Ospedale Pediatrico Bambin Gesù in Rome, will present how his laboratory has reduced sample-to-sample variability by adopting an automated NGS library preparation workflow. In particular, he will describe:

  • The process leading to the automation of the Nephropathies Solution (NES) by Sophia Genetics on the PerkinElmer Sciclone G3 NGS workstation
  • The analytical performance of the automated workflow versus the manual one
  • The application of the automated NES in resolving a complex clinical case  
Sponsored by

Chief Scientific Officer, TOMA Advanced Biomedical Assays, Impact Lab Group  

This webinar discusses cell-free DNA prenatal screening in the era of genome-wide sequencing and factors influencing the clinical utility of expanded noninvasive prenatal testing (NIPT) menus.

NIPT by cell-free DNA analysis is recognized as the most effective method of prenatal screening for trisomies 21, 18 and 13, but the clinical utility of NIPT for rare and uncharacterized genomic imbalances is largely unknown. In order to understand how expanding uses of this technology may impact clinical care, laboratories and clinicians must understand what type of results to expect and the biological and technical factors that may influence the accuracy of these results.

In this webinar, Dr. Francesca Romana Grati of TOMA Advanced Biomedical Assays reviews the current state of NIPT technologies as well as their expanding applications into rare and uncharacterized genomic disorders.

Dr. Grati discusses:

  • Currently available NIPT technologies
  • Differences in genome-wide and targeted NIPT
  • Biological and technical factors that influence the accuracy of NIPT results
  • The clinical impact of screening for rare and uncharacterized genomic imbalances with NIPT
Sponsored by
Tue
Jun
18
1:00 pm2019
Sponsored by
ArcherDX

Clinical Genomics of NTRK Fusion Detection in Cancer

GenomeWebinar

Associate Director, Laboratory for Molecular Pediatric Pathology; Staff Pathologist, Boston Children's Hospital; Instructor of Pathology, Harvard Medical School

This webinar discusses background and clinical genomics of NTRK fusion detection in cancer. NTRK fusions are the focus of new therapeutic options, but clonal and subclonal lesions are notoriously difficult to detect. This webinar provides an overview and background about the increased role of these fusions, and latest trends in diagnosis, prognosis, and treatment, as well as a research case study on detection.

Join Dr. Alanna Church of the Laboratory for Molecular Pediatric Pathology and Staff Pathologist at Boston Children's Hospital to learn more about the increasing role of NTRK fusions:

  •  Overview and background of fusion mutations, specifically NTRK 1, 2, and 3
  •  Frequency overview and specificity needed for detection
  •  Overview of research case of utilizing NGS technology in detection.
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

Test Engineer, Ginkgo Bioworks

Ribosomal ribonucleic acid (rRNA) accounts for up to 99 percent of the total RNA depending on the cell type. Therefore, it’s critical to deplete this highly abundant RNA prior to doing RNA-seq experiments to maximize coverage of target RNA and improve sequencing economy. There are different commercial bead-based rRNA depletion or polyA enrichment kits. However, both methods are inefficient and introduce 3’ biases.  In addition, they are limited to only certain species.

This webinar discusses a species-specific rRNA depletion method that uses the Kapa RNA HyperPrep Kit with RiboErase in combination with customized oligonucleotides. The method enables enrichment of sequencing reads on low-abundance transcripts. In addition to lowering cost by sequencing target RNA, this depletion method generates a more comprehensive transcriptome that retains precursor mRNAs and non-coding RNAs.

Join this webinar to learn:

  • How to generate species-specific rRNA probes for optimal rRNA depletion
  • How to decrease the cost of RNA-seq by enriching for only the RNA that matters
  • How to generate more comprehensive transcriptome data
  • How to generate RNA-seq data from degraded RNA
Sponsored by
Tue
Jun
11
11:00 am2019
Sponsored by
Roche

The Promise of Liquid Biopsy in Lung Cancer Monitoring

GenomeWebinar

Head of the Cancer Genome Research Division; German Cancer Research Center

This webinar provides an overview on the potential for liquid biopsy approaches to monitor therapy resistance in lung cancer.

Lung adenocarcinoma is the most prevalent subtype of lung cancer and characterized by considerable morphological and mutational heterogeneity, which is the primary source of therapy resistance and tumor progression. For many targeted treatments, the underlying molecular alterations leading to therapy resistance are well established. However, frequent tissue sampling to verify such alterations and adapt treatment strategies is not possible. Liquid biopsy approaches are potentially appropriate to overcome these obstacles: Circulating tumor DNA might be superior to tissue biopsies in representing tumor heterogeneity. In addition, frequent blood draws are feasible to monitor molecular alterations even in research subjects who suffer from substantial comorbidities.   

In this webinar, Dr. Holger Sültmann of the German Cancer Research Center discusses liquid biopsy approaches to monitor lung cancer progression using tumor markers in the blood. The focus will be on nucleic acid mutation detection and quantification in clinical samples and their relevance for diagnostics.

The webinar also addresses strengths and limitations of PCR- and NGS-based analysis technologies.

Sponsored by
Thu
Jun
6
1:00 pm2019
Sponsored by
NRGene & Illumina

Accelerating Crop Research with High-Quality Affordable Genome Assemblies

GenomeWebinar

School of Plant Sciences and Food Security, Institute for Cereal Crop Improvement (ICCI); Tel Aviv University 

Director of DNA Services, University of Illinois at Urbana Champaign

This webinar discusses the impact of affordable de novo genome assemblies on crop research.

De novo genome references are critical to understanding plant biology and unlocking the potential of genomics for cutting-edge plant breeding in agriculturally important species. However, assembling quality references from sequencing data can be a costly, complex, and time-consuming process.

In this webinar, Assaf Distelfeld from Tel Aviv University, a world leader in wheat genomic research, discusses recently generated genome assemblies of wheat progenitors, and how this new resource can help solve biological questions and improve wheat breeding. In addition, representatives of NRGene, Illumina, and the University of Illinois at Urbana Champaign detail how their technology and services helped make this project happen, and others like it.

The recent decrease in short-read sequencing costs and increased read lengths on the Illumina Novaseq sequencer and SP flow-cell, combined with NRGene’s accumulated experience in wheat genomics and bioinformatics, resulted in a more than 50 percent reduction in project cost. These innovations make de novo sequencing more accessible and affordable for researchers than ever before, without compromising genome assembly quality. 

Sponsored by
Tue
Jun
4
1:00 pm2019
Sponsored by
NanoCellect

A CRISPR Study to Decipher the Role of Genetic Risk Variants in Glaucoma

GenomeWebinar

Assistant Professor of Ophthalmology, University of California San Diego, Shiley Eye Institute

This webinar will discuss a study that used CRISPR/Cas9 to engineer mice harboring risk variants associated with glaucoma in order to assess their functional relevance. 

Glaucoma is a group of diseases with diverse molecular mechanisms of pathogenesis, all of which converge on a common pathway leading to typical optic nerve damage, loss of retinal ganglion cells, and consequently loss of vision. Retinal ganglion cells (RGCs) are the brain’s only connection to the outside world and, despite numerous studies, there is not yet a successful therapy to prevent their loss in glaucoma. Recent advances in genomics have allowed researchers to describe the association between the risk of glaucoma and specific genomic loci. Several studies have identified the nonsynonymous coding variant SIX6-(rs33912345 His141Asn) as strongly associated with glaucoma.

Our speaker, Dorota Skowronska-Krawczyk, PhD, will discuss an effort that sought to directly assess the functional relevance of the SIX6 risk variant in eye function. Dr. Skowronska-Krawczyk and colleagues used CRISPR/Cas9 technology to engineer mice harboring human risk variants and non-risk variants of SIX6. They then used immunostaining and visual evoked potential approaches to determine that the SIX6-His variant is indeed causing more cell death and vision loss.

Dr. Skowronska-Krawczyk will discuss how her team used NanoCellect’s WOLF Cell Sorter to sort the RGCs required for this study. The live, purified RGCs, isolated from retinas three days after intraocular pressure elevation, were assessed for transcriptional and epigenetic changes in the context of the SIX6 genetic variant. Sample preparation steps and bioinformatic analysis of the findings will also be presented.

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
Tue
May
21
11:00 am2019
Sponsored by
Qiagen: Nov 16, 2014

Implementation of qPCR Mutation Assays for Routine Use in a Hematology/Oncology Lab

GenomeWebinar

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
Mon
May
20
11:00 am2019
Sponsored by
Qiagen: Nov 16, 2014

Respiratory Viruses: Considerations for Multiplex Testing from the Lab to Point of Care

GenomeWebinar

Associate Professor;
Laboratory of Virology, Bichat-Claude Bernard Hospital

This webinar will discuss considerations that labs need to take into account when adopting rapid multiplex PCR testing for respiratory viruses in the clinical setting.

The development of rapid multiplex PCR tests enables the detection of almost all respiratory viruses in a few hours. These tests provide a deeper understanding of respiratory viruses' epidemiology among children or adults, as well as community- or hospital-acquired infections. They also allow clinicians to consider viral etiology to improve isolation management, antibiotic use, or a patient’s length of stay.

While these tests offer clear benefits for some patient populations, labs looking to adopt rapid multiplex PCR testing must balance their costs against the impact on patient care.

In this webinar, Dr. Benoit Visseaux of Bichat Claude Bernard Hospital, a university hospital in Paris, will discuss his experience with multiplex PCR testing for respiratory viruses. Dr. Visseaux will discuss the implementation of these tests in the context of improving patient 

Sponsored by

Scientist, R&D Department, Illumina

This webinar will discusses 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 focuses 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
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 discusses 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 testing. 

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

This webinar shares data supporting the use of CytoScan XON to test multiple genes for intragenic CNVs in the human genome and demonstrates 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

Associate Professor, Biomedical Engineering, Yale University

Director, New Collaborations, Isoplexis

This webinar discusses 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, discusses IsoPlexis’ advanced immune-based approaches in systemic lupus erythematosus and adverse events like cytokine release syndrome and neurotoxicity in cell therapy. He describes 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 shares 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