GenomeWebinars

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

Chief Medical Officer, ResearchDx

This webinar will detail a comprehensive strategy that a lab has put in place to evaluate  NGS oncology assays for genomic tumor profiling of plasma and tissue samples.  

The growing adoption of next-generation sequencing (NGS) technologies is enabling many labs to perform NGS-based tumor profiling inhouse. Today, genomic tumor profiling can be accomplished using DNA extracted from tumor tissue samples, as well as by liquid biopsy approaches using circulating tumor DNA (ctDNA) in plasma samples. The question of what labs need to consider when choosing the right solution for their research needs is of great interest. 

In this webinar, Dr. Shelly Gunn, Chief Medical Officer of ResearchDx, will present an overview of  their lab’s approach to establishing optimized ctDNA and formalin-fixed, paraffin-embedded (FFPE) tissue workflows for in-house clinical research testing. Dr. Gunn’s presentation will:

  • Describe the process of  implementing new NGS tumor tissue and ctDNA oncology assays, including learnings from optimizing both ctDNA and FFPE tissue workflows;
  • Discuss areas that are important for achieving high technical performance and accurate results, such as QC methods, barcoding, and hybrid capture vs. amplicon technology;
  • Summarize areas of research where the combination of these technologies could be applied.

The AVENIO ctDNA Analysis Kits and AVENIO Tumor Tissue Analysis Kits are for research use only, and not for use in diagnostic procedures.

AVENIO is a trademark of Roche.

Sponsored by
Mon
Nov
5
11:00 am2018
Sponsored by
Sophia Genetics

Overcoming Challenges in Solid Tumor Testing with Advanced AI

GenomeWebinar

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

Associate Professor, Department of Pathology; Augusta University

This webinar will provide a first-hand look at how a leading pathology lab implemented a next-generation sequencing panel to capture comprehensive molecular tumor profiles.

As cancer genetics evolves and new clinical trials and data emerge, it has become increasingly critical to detect single nucleotide variants, insertions and deletions, as well as measuring copy number variations, microsatellite instability, and tumor mutational burden.

NGS serves as an important tool for such interrogations, but major gaps remain in performance robustness and interpretation algorithms. The implementation of a single assay, combined with an integrated bioinformatics pipeline, that assesses SNVs, indels, CNVs, MSI, and TMB enables efficiencies in sample usage, time, and cost.

Our speaker, Dr. Ravindra Kolhe of Augusta University, will discuss his experience using the new QIAseq Tumor Mutational Burden panel coupled with QIAGEN’s bioinformatic solutions in comparison with a centralized testing model, focusing on:

  • QIAseq TMB panel content
  • Bioinformatics pipeline
  • Ease of adoption/integration
Sponsored by
Thu
Nov
8
11:00 am2018
Sponsored by
Horizon Discovery

Defining the Performance Characteristics of New NGS Assays with Reference Standards

GenomeWebinar

R&D Coordinator, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania

Bioinformatics Specialist, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania

This webinar will provide a practical approach to using reference standards to define the performance characteristics of new next-generation sequencing assays during validation.

In this webinar, Robyn Sussman and Ashkan Bigdeli from the Center for Personalized Diagnostics at the University of Pennsylvania will discuss how they used reference standards as part of the validation workflow for their NGS assays.

In one case, they used standards with varying degrees of damage to validate a low-input assay that can accommodate highly compromised formalin-fixed, paraffin embedded tissues.

Sussman and Bigdeli validated a small, amplicon-based sequencing panel to accommodate the low-yield and low-quality specimens that do not qualify for larger sequencing panels. The team used Horizon’s Quantitative Multiplex Reference Standard gDNA along with Quantitative Multiplex Formalin Compromised DNA (Mild, Moderate and Severe) to assess the input requirements for the assay and the performance characteristics of samples with varying DNA quality.

For larger panels with whole coding sequencing coverage, copy number changes to specific genes can be predicted algorithmically. The University of Pennsylvania team will also discuss how they validated a copy number caller for a solid tumor sequencing panel. For this project, they used Horizon’s Structural Mutliplex Reference Standard gDNA and Structural Multiplex FFPE Reference Standard to define the performance characteristics of the caller, which will be used for both fresh and paraffin-embedded tissue.

Sponsored by
Tue
Nov
13
1:00 pm2018
Sponsored by
Sunquest

Delivering on Precision Medicine at Children’s National Health System

GenomeWebinar

Medical Geneticist, Children’s National Medical Center; Assistant Professor, George Washington University

Manager, LIS, Laboratory Medicine & Pathology,
Children’s National Medical Center

This webinar will provide a detailed overview of how a leading children’s hospital made precision medicine part of its standard of care for rare disorders.

Children’s National Health System, located in Washington, DC, is one of the top five children’s hospitals in the country, according to US News & World Report. Starting initially by bringing genetic testing in-house for enhanced care quality and efficiency, the system’s Laboratory Medicine and Genetics & Metabolism divisions now make up one of the largest clinical genetics programs in the United States, bringing precision medicine diagnostics and therapeutics to children with rare disorders.

In this session, you will learn how Children’s National Health System:

  • Made clinical and technical considerations before bringing genetic testing in-house
  • Evaluated challenges and opportunities associated with starting and scaling an in-house genetic testing program\
  • Launched a first-of-its-kind center to target care and treatment of children with rare disorders.
Sponsored by

Vice President, Immunology, 
Caprion Biosciences

Flow cytometry is one of the most valuable and versatile tools for multiparametric, single-cell analysis. More recently, flow cytometry has become an integral component of the drug discovery and development process as novel therapeutic approaches targeting the immune system are being applied in oncology and infectious diseases. Flow cytometry data supporting manufacturing as well as safety and efficacy during clinical evaluation are critical components of biological license applications submitted to regulatory agencies.

As the technology advances and the applications of flow cytometry expand, it is increasingly important to ensure that measurements are made precisely and with certainty. In flow cytometry the quality pillars for building measurement assurance include: instrument characterization and standardization; developing and validating high quality methods; and monitoring instrument and assay performance. In the past few years, significant progress has been made in all three areas due to the efforts of the National Institute of Standards and Technology, the US Food and Drug Administration, the American Association of Pharmaceutical Scientists, the International Society for Advancement of Cytometry, and the International Clinical Cytometry Society.

This webinar will provide updates on the current best quality practices in flow cytometry for drug discovery and development and will provide specific case studies in the area of immunotherapy development.

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
Sponsored by
Tue
Nov
27
1:00 pm2018
Sponsored by
Genialis & Roche

Defining a Multi-Omics Target Discovery Framework for High-Risk Cancers

GenomeWebinar

Assistant Professor, Pediatrics-Oncology,
Baylor College of Medicine

While next-generation sequencing (NGS) has driven recent advances in precision oncology research, it often falls short when identifying the molecular mechanisms underlying many malignancies. As a result, alternative NGS-based approaches are needed to identify oncogenic drivers and potential drug targets.

To address this challenge, Stephen Mack of Baylor College of Medicine has developed a novel approach to assess transcriptional and epigenetic regulatory activity in chemotherapy-resistant brain tumors. In this webinar, he will define a framework for integrating multi-omics NGS data to discover and confirm novel drug targets in high-risk neurological cancer models.

Using tumor glioblastoma, ependymoma, and diffuse intrinsic pontine glioma models, Dr. Mack will demonstrate how integrative analysis of H3K27ac ChIP-seq and RNA-seq data enabled his team to identify molecular pathways that can be inhibited by small-molecule drugs.

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

Sponsored by
Thu
Nov
29
1:00 pm2018
Sponsored by
Schott

Glass or Polymer? A Comparison for Use in In Vitro Diagnostic Biochips

GenomeWebinar

Bijlard Technologies, Technogation BV

Business Development Manager,
Schott Nexterion

This webinar will discuss how understanding the relative performance characteristics of glass and polymer substrates for in vitro diagnostic applications such as microarrays and microfluidics can help to optimize diagnostic performance.

Interest in in vitro diagnostics has exploded in the last years as advances in molecular diagnostics promise to improve patient health. In this webinar, two experts on biochip development — Richard Bijlard of Technogation and James Downs of Schott Nexterion — will discuss key factors that should be considered for substrate material choices when developing an in vitro diagnostic consumable.

What will you learn?

  • Overview of various materials used for the production of in vitro diagnostic consumables
  • Design considerations: strengths and weaknesses of various substrates in relation to their applications
  • Market and technological trends in substrate use.
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

GenomeWebinar

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

Executive Director of R&D and Translation Medicine,
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, Executive Director of R&D and Translation Medicine 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
Sponsored by
Recent GenomeWebinars
Mon
Oct
22
1:00 pm2018
Sponsored by
Agena Bioscience

Implementation of Molecular Sample Tracking to Ensure Sample Identity and Integrity

GenomeWebinar

Vice President of Clinical Operations, Ambry Genetics

This webinar discusses a solution for ensuring sample identity and integrity for complex molecular testing workflows.

Clinical diagnostic testing in a CLIA/CAP laboratory involves comprehensive sample tracking from sample receipt to wet lab preparation and result interpretation. However, even with the most rigorous lab consumable barcoding and sample-tracking system, a patient sample could still encounter a rare mislabeling or mishandling prior to receipt or during preparation in complex laboratory workflows.

In this webinar, Dr. Sharon Mexal, VP of Clinical Operations at Ambry Genetics, shares her team’s experience with integration and scale-up of the iPlex Pro Sample ID panel from Agena Bioscience. Her talk discusses the use of the system for cost-effective sample tracking and NGS data quality assurance or germline hereditary testing.

Sponsored by
Wed
Oct
17
12:00 pm2018
Sponsored by
Lexogen

Reliable RNA-Seq Expression Profiling from Low-Quality FFPE Biobank Samples

GenomeWebinar

Assistant Professor, Division for Bioinformatics, Biocenter, Innsbruck Medical University; Scientific Support, NGS core facility, Innsbruck Medical University

This webinar will present a method for RNA-seq expression analysis of FFPE-derived RNA samples that are too degraded for successful application of standard RNA-seq techniques.

Biobanks consisting of formalin-fixed, paraffin-embedded (FFPE) patient samples, collected over decades, present unique opportunities for studying gene expression in large cohorts of patients with a given disease. This approach, however, has been limited by the high degree of RNA degradation in FFPE-derived samples, in some cases leading to more than half of the biobank samples being discarded.

This webinar will introduce a method for successfully generating libraries and analyzing FFPE-derived RNA samples so degraded that less than 20 percent of the RNA fragments have a length above 200 nucleotides. Our speaker, Anne-Margrethe Krogsdam Christensen of Innsbruck Medical University, will discuss a comparison of the results from FFPE samples and matched fresh-frozen samples, and finally across a cohort of patient cancer samples.

Dr. Krogsdam Christensen will explain how her team has been able to generate viable libraries and quality sequencing data, regardless of the degree of degradation, thereby strongly pushing the limits for FFPE samples that can be included in analysis.

Sponsored by
Thu
Oct
11
11:00 am2018
Sponsored by
ArcherDX

Validation of Error-Corrected Sequencing for Hematological Malignancies

GenomeWebinar

Director, Duke Cytogenetics Laboratory
Associate Director, Duke Molecular Diagnostics Laboratory
Duke University Health System

Assistant Director, Clinical Cytogenetics and Molecular Diagnostics Laboratories,
Duke University Health System

This webinar discusses a validation study for a next-generation sequencing (NGS) assay for hematological malignancies (e.g., acute myeloid leukemia, acute lymphocytic leukemia, myelodysplastic syndrome, and myeloproliferative neoplasms).

Diagnostic and prognostic testing methodologies in hematological malignancies are evolving beyond traditional chromosome analysis, fluorescent in situ hybridization, and single-analyte molecular testing toward NGS because it enables the detection of multiple molecular driver mutations and oncogenic fusions in a single assay. However, most NGS approaches are limited in their ability to detect fusions, or to detect known pathogenic variants in specific genes such as CEBPA and FLT3 without using additional molecular methodologies. The ability to quickly and accurately identify specific translocation partners and the presence of specific pathogenic variants is critical in the era of increasingly personalized treatment plans.

In this webinar, Drs. Catherine Rehder and Sarah Rapisardo at Duke University describes their efforts to validate the Archer VariantPlex Myeloid assay. They  also discuss their work to expand testing with a custom Archer FusionPlex assay to detect known and novel fusions, with a focus on Ph-like ALL fusions.

Drs. Rehder and Rapisardo detail their initial proof-of-principle studies, which have demonstrated 100 percent concordance with their current assays, with superior coverage of previously problematic regions and significant improvements in library complexity.

 

ArcherDX, Inc. is committed to protecting and respecting your privacy, and we’ll only use your personal information to administer your account and to provide the products and services you request from us. By registering for this webinar, you agree to receive occasional communications from ArcherDX. You may unsubscribe from these communications at any time using the link provided in every email from ArcherDX.

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. 

Sponsored by

Assistant Director, Genomics Shared Resource,
Roswell Park Comprehensive Cancer Center

This webinar will discuss a comparison of several different library preparation methods for whole-exome sequencing of formalin-fixed paraffin embedded (FFPE) tissue.

FFPE procurement is the standard for tumor banking and remains part of the clinical standard of care. These samples provide an excellent opportunity to advance cancer research with well characterized histological and pathological annotation combined with extensive clinical data.

The ability to use archival FFPE samples to screen entire exomes for both known and novel mutations will have a strong impact on clinical and basic research initiatives, but the use of DNA extracted from FFPE for whole-exome sequencing (WES) is presently limited. The pre-capture PCR step within the WES protocol is the most critical when working with degraded samples, which can therefore significantly affect the quality of sequencing data.

In this webinar, Prashant Singh of the Roswell Park Comprehensive Cancer Center will discuss his team's project to test several different methods for adding adaptors (pre-capture PCR) within the WES protocol. Dr. Singh will share the results of the comparison and the impact of this work on downstream analysis.

Sponsored by

Hospital Practitioner, Laboratory of Molecular Genetics, Arnaud de Villeneuve Hospital

 

This webinar will discuss the use of new software tools to support the diagnosis of CTFR-related disorders using next-generation sequencing.

Molecular diagnosis of cystic fibrosis and CFTR-related disorders is based on the detection of mutations in the CFTR gene. A wide range of techniques is still used to identify CFTR gene sequence variations. While there is no gold standard or preferred method for routine testing, the rapid adoption of NGS technologies in diagnostics laboratories is enabling a range of new approaches. 

In this webinar, Caroline Raynal of the Laboratory of Molecular Genetics at Arnaud de Villeneuve Hospital will describe how her team tested a new data analysis software in combination with a diagnostic amplicon-based CFTR assay for NGS.

The lab re-analyzed 13 runs in which 158 individuals were included (patients, relatives, partners, and fetuses suspected to have CF) and assessed the assay with the new software.

This webinar will provide details on the findings of this study as well as how amplicon-based solutions for NGS in diagnostics can provide reliable results.

Sponsored by

Director of Molecular Pathology, Carolinas Pathology Group

Director of Molecular Pathology, Phenopath Laboratories

In the last few years several molecular testing methodologies — such as immunohistochemistry, PCR, and sequencing — have been approved by the US Food and Drug Administration to aid in the management of patients with lung cancer.  

In this webinar you’ll learn how these very different technologies serve specific needs and how creating a testing strategy that employs many of these different methodologies can provide the information clinicians need to make the best treatment decisions for critically ill patients.

Our two speakers, Dr. John Longshore from the Carolinas Pathology Group and Dr. Harry Hwang from Phenopath Laboratories, will share their experiences from both the large healthcare system and reference laboratory perspectives.

Sponsored by

Data Scientist,
National Center for Biotechnology Information/University of Maryland Baltimore

This webinar will provide an overview of some efforts underway at the National Center for Biotechnology Information to help improve scientific reproducibility in genomics research.

Scientific reproducibility relies on literature, data, and code. While biological literature is becoming more open, and data is becoming more widely shared, code written in a biomedical context is often not reproducible.

In many scientific disciplines, the rapidly emerging datasets exceed the available resources of traditional software development communities. Fueled by this shortage and aided by increasingly powerful scripting languages, domain experts often turn to their own devices, which can create difficulties in reproducibility because of issues with documentation, ongoing development, and advertising.

This session will describe efforts NCBI has undertaken to address these issues, including NCBI-facilitated hackathon programs (with some teams working on modular, reproducible workflow generators), “analyze-athons,” reproducibility workshops, student discovery challenges, and the scale-up of data science training worldwide.  

For more information on other webinar in this series, click here.

Sponsored by

Quality & Training Manager NHS Fife

This webinar will share how a medical microbiology lab within the UK’s National Health Service introduced new systems and workflows to improve its efficiency without impacting the quality of its service.

Modern medical microbiology labs have to do more with less: They are tasked with processing more samples and generating more results, in less time than before and with less resources, all without impacting the quality of their output. Without continuous improvement, labs risk failing some or all of these aspects and, more importantly, failing their patients.

Faced with this challenge, the medical microbiology lab at Victoria Hospital of Fife, Scotland, worked in partnership with its suppliers to develop and implement new instrument workflows, new molecular diagnostic assays, and new ways of working to improve its efficiency.

In this webinar, Dr. Mairiead MacLennan of Victoria Hospital will detail how this effort not only made the lab more effective for today, but also provided additional capacity for the future. Dr. MacLennan will also present how the lab achieved this while improving its output and improving patient care.

Sponsored by
Wed
Sep
26
11:00 am2018
Sponsored by
PerkinElmer

Implementation and Validation of a High-Precision, Non-NGS NIPT Platform

GenomeWebinar

Professor of Pathology and Laboratory Science
Women & Infants Hospital
Alpert Medical School at Brown University

Project Manager,
Cerba Xpert

Chief Technology Officer, Co-Founder,
Vanadis Diagnostics, a PerkinElmer company

This webinar will provide a comprehensive overview of an automated, high-precision non-invasive prenatal testing (NIPT) platform that does not rely on next-generation sequencing or PCR amplification, enabling precise measurement of chromosomal aneuploidies for high performance screening minimizing both false positives, false negatives and no-calls.

In this webinar, three speakers will provide different perspectives on the Vanadis NIPT platform and its implementation in the lab setting.

First, Fredrik Dahl, chief technology officer of Vanadis, will provide a brief outline on the system and will discuss supporting clinical data on both high- and low-risk cohorts. Dr. Dahl will provide details of how Vanadis differs from NGS-based NIPT systems as well as clinical proof-of-principle data.

Glenn Palomaki of the Alpert Medical School at Brown University will then provide an update on an external research study of the Vanadis system in the US. The study, called VALUE (Validation of a Lower Cost Aneuploidy Screen), aims to enroll 2,400 women from the general pregnancy population and 250 high-risk pregnancies. Along with screening performance characteristics (detection rate, false positive rate, and test failure rate), the study is collecting information on turn-around-time, costs of equipment and supplies, and needed training.

Finally, Jérémie Gautier of Cerba Xpert will discuss a validation study using the Vanadis NIPT system. Dr. Gautier will outline his laboratory’s experience of the installation process, training, and the day-to-day activities involved in operating the system.

Vanadis® NIPT is in development 

Sponsored by

Molecular Pathology Department;
University Hospital Dijon

This webinar describes the implementation of a digital PCR system in an academic hospital setting to manage the treatment of cancer patients.

Benjamin Tournier, from the molecular pathology department of University Hospital Dijon, will share details of his lab's liquid biopsy setup, which is using the Naica 3-color Crystal Digital PCR system from Still Technologies to manage melanoma and lung cancer patients under targeted therapy.

Attendees of this webinar will:

  • Gain a better understanding of the liquid biopsy process for metastatic melanoma and lung cancer patients
  • Understand the Naica System workflow and its advantages
  • Learn the benefits of digital PCR for the detection of circulating tumor DNA, circulating tumor cells, and circulating tumor exosomes in liquid biopsy
  • Understand the advantages of digital PCR for monitoring patients and their treatment
Sponsored by
Thu
Sep
20
1:00 pm2018
Sponsored by
St. Jude Children's Research Hospital

Cloud-based Data and Analysis Tools Yield Novel Insights for Cancer Research

GenomeWebinar

Professor and Associate Director of Computational Biology,
Jackson Laboratory of Genomic Medicine

Manager of Bio Info Software Development,
St. Jude Children's Research Hospital

Group Lead, Bioinformatics Analysis,
St. Jude Children's Research Hospital

This webinar will provide an overview of how St. Jude Cloud, a public repository of pediatric cancer genomics data and analysis tools, is impacting cancer research.

Developed in partnership with Microsoft and DNAnexus, the St. Jude Cloud offers next-generation sequencing data and analysis tools in a secure cloud-based environment. Access to data is simple, fast and does not require downloading prior to exploration. Researchers can also upload their own data in a private, password-protected environment to use the St. Jude Cloud visualization and analysis tools.

In this webinar, Scott Newman, biological lead, and Clay McLeod, lead developer of St. Jude Cloud, will provide an overview of this platform, which includes more than 5,000 whole-genome, 5,000 whole-exome, and 1,200 RNA-seq datasets from more than 5,000 pediatric cancer patients and survivors. They will also demonstrate the collection of bioinformatics tools and visualizations to help both experts and non-specialists gain novel insights from genomics data.

In addition, Roel Verhaak of the Jackson Laboratory for Genomic Medicine, will discuss how his lab is using the whole genome sequencing datasets available on the Cloud to study the processes that underlie treatment resistance and progression in brain tumors.

Sponsored by
Wed
Sep
19
11:00 am2018
Sponsored by
Agena Bioscience

A Comparison of Two Liquid Biopsy Approaches in Advanced Lung Carcinoma

GenomeWebinar

Medical Director,
Laboratoire de Biologie Medicale,
Imagenome

This webinar will discuss a study to compare two different liquid biopsy approaches — one based on real-time PCR and one based on mass spectrometry — in patients with advanced lung cancer.

With liquid biopsy entering the routine in personalized cancer treatment it is important to understand the differences inherent to technologies for analyzing circulating tumor DNA (ctDNA) and its implication for the patient.

The study is using both a real-time PCR assay and a MALDI-TOF assay on blood samples taken from patients with advanced lung cancer at time of diagnosis or during follow-up of treatment by EGFR inhibitors.

Initial results demonstrate that the MassArray UltraSeek Lung panel is a sensitive and accurate technology for ctDNA analysis and that this sensitive method could potentially detect more patients with EGFR mutations who could benefit from a targeted therapy — particularly at the time of diagnosis.

Sponsored by
Tue
Sep
18
11:00 am2018
Sponsored by
Horizon Discovery

Validation and Internal QC of Clinical NGS to Support an Accredited Diagnostic Workflow

GenomeWebinar

Head of Bioinfomatics, Sarah Cannon Molecular Diagnostics

In this webinar, Kevin Balbi, head of bioinformatics at Sarah Cannon Molecular Diagnostics, will discuss the validation of targeted sequencing panels on the Ion Torrent platform using Horizon Discovery’s Tru-Q controls. He will also discuss how those controls are being used for ongoing internal quality control (IQC) and how this has supported a recent laboratory inspection by the United Kingdom Accreditation Service under ISO15189.

Sarah Cannon Molecular Diagnostics, part of HCA Laboratories in London, offers a range of molecular assays, from single-gene variant analyses through to a 50-gene panel somatic variant analysis, MLH1 promoter hypermethylation, T & B cell clonality assessment, and microsatellite instability status.

Validation of targeted sequencing panels for clinical diagnostic use requires reference material with a range of known variants and confirmed variant frequencies. Additionally, the continual assessment of assay performance is key to ensuring robust and reliable results.

Dr. Balbi will demonstrate how his team has validated three targeted DNA sequencing panels for clinical diagnostic use and assessed their limit of detection using the Horizon Discovery Tru-Q controls. He will explain the lab's approach to IQC, also showing the reliability of the assays over time. These data contributed to the accreditation of the bioinformatics workflow under ISO15189.

Sponsored by

Senior Lab Manager,
LifeLabs Genetics

Senior Scientific Director,
Research Animal Diagnostic Services,
Charles River Laboratories

Global Product Support Manager,
Agena Bioscience

This webinar will share details of how two large reference and service laboratories have rapidly deployed highly multiplexed genotyping assays to meet their clients' testing needs.

Our first speaker, Connie Lisle from LifeLabs Genetics, the largest clinical laboratory in Canada, will discuss various pharmacogenetics panels her lab has developed on the MassArray system.

Our second speaker, Dr. William Shek from Charles River Laboratories, a pre-clinical and clinical laboratory service provider, will share his laboratory’s experience with developing preclinical assays on animal models to support drug discovery and development with the MassArray system.

Sponsored by
Wed
Sep
12
11:00 am2018
Sponsored by
Qiagen

T-Cell Receptor Sequencing for Melanoma Immunotherapy Monitoring

GenomeWebinar

Inserm Research Director, Tumor Immune Responses and Immunotherapy
Inserm Cancer Research Center

Researcher, Tumor Immune Responses and Immunotherapy
Inserm Cancer Research Center

This webinar will discuss ongoing work to apply T-cell receptor sequencing (TCRseq) approaches to immunotherapy monitoring for melanoma patients.

Despite its undisputed superior clinical efficacy compared to chemo- or radiotherapy, anti-PD-1 monotherapy remains inefficient on more than 60 percent of cancer patients. Acute toxicities are less common than those reported for anti-CTLA-4 therapy but remain an appreciable risk for patients. For these reasons, defining early and robust predictive markers of clinical response is crucial both to improve patient management and to reduce treatment costs. Furthermore, the comprehensive analysis of PD-1 regulation and signaling will also have a considerable impact on the optimization of other immunotherapies such as T-cell-based immunotherapies.

In this webinar, researchers from the Inserm Cancer Research Center in Nantes, France, will share findings from studies seeking to understand the molecular mechanisms regulating PD-1 expression in melanoma-specific T lymphocytes. Their work points toward methods for monitoring the immune responses of cancer patients treated with anti-PD-1 antibodies as well as for the selection of optimal effector T cells for adoptive cell transfer treatments.

The presentations will offer new prospects for patient monitoring based on TCRseq approaches.

Sponsored by
Wed
Aug
29
1:00 pm2018
Sponsored by
Canon BioMedical

Implementing Novel Technologies in the Core Lab: Spatial Transcriptomics and Sci-MET

GenomeWebinar

Chief Operating Officer, Spatial Transcriptomics

Next Generation Sequencing and Single Cell Genomics Platform Head, Functional Genomics Center Zurich

PhD Candidate, Oregon Health & Sciences University

This webinar will discuss two potentially disruptive technologies — spatial transcriptomics and single-cell methylome combinatorial indexing (sci-MET) — along with considerations for implementing them in a core facility setting.

Spatial transcriptomics combines traditional histological information with genome-wide transcriptome data by using high-resolution tissue imaging and RNA capture. This is made possible by placing thin tissue sections on microscopic glass slides, which are covered with spatially barcoded cDNA primers. Researchers using this technology have produced high-quality data from a variety of tissue types (for example brain, breast cancer, prostate cancer and heart) and organisms (human, mouse, and plants) and spatially barcoded arrays have also been applied to study single cells in solution.

Single-cell combinatorial indexing (sci-) is a robust and generalizable protocol family developed for the interrogation of single-cell omics. Sci- protocols follow a shared strategy of forming a unique barcode per nuclei through multiple iterations of indexing, pooling, and random sampling. With this method, protocols for single-cell library generation assaying the transcriptome, chromatin accessibility, genome-wide copy-number variation, chromatin conformation, and most recently, the methylome have been described. The methylome protocol (sci-MET) was used to generate 3,282 high-quality single-cell whole-genome methylation libraries. With low coverage, sparse methylation information was shown to be sufficient in discriminating cell types, both in a synthetic mixture of cell lines and in a neuronal subtype from mouse cortical samples. Sci-MET, as well as the other sci- protocols, provide an avenue for high-throughput single-cell omics necessary to interrogate the nuance and complexity of complex and developing tissue. 

In this webinar, our panelists will discuss specifics of these technologies and their applications, within a particular focus on their implementation in core facilities.

For more information on other webinar in this series, click here.

Sponsored by

Assistant Professor, Department of Molecular and Human Genetics; Human Genome Sequencing Center, Baylor College of Medicine

Luke Stewart, BS, Senior Manager, Field Applications, Fluidigm Corporation

This webinar shares details of how the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine implemented a sample identity assay as part of its next-generation sequencing (NGS) workflow.

The importance of ensuring sample integrity and quality from sample acquisition to final data analysis and delivery is a shared concern among researchers involved in clinical and translational research — particularly with complex, multiphase studies.

The HGSC generates data to support numerous research programs that require rapid delivery of high-quality sequencing data. To ensure end-to-end sample and data integrity, the HGSC has implemented the Fluidigm SNP Trace assay to confirm sample identity in its workflow. 

In this webinar, Jianhong Hu describes the HGSC’s high-throughput sequencing and reporting pipeline and discuss how the center has integrated sample identification into its overarching workflow. Luke Stewart, Senior Manager of Field Applications at Fluidigm, concludes the discussion with information on new advancements in sample identification offered by Fluidigm.

Sponsored by

Founder, AdvaGenix

This webinar offers a look at how an advanced genetics laboratory implemented and validated a commercial bioinformatics system to help scale its operations. 

William Kearns, founder of genetics testing lab AdvaGenix, shares his team's experience as it sought to increase its testing throughput while maintaining high quality standards. After studying the time and cost associated with building and validating a bioinformatics platform from scratch, as well as the cost of maintaining such a system, the AdvaGenix team decided to look for commercial solutions. 

AdvaGenix needed a solution that adhered to society guidelines and also included domain expertise in genetic testing. The team ultimately opted for a system from Qiagen and has since been able to scale up its operations by at least 25-fold.  Dr. Kearns discusses his team's experience and learnings from this implementation and the results they have seen so far.

Sponsored by

Chief Operations Officer,
Institute for Protein Innovation 

This webinar will discuss an automated, high-throughput method of generating high-quality antigens and antibodies.

James D. Love, Chief Operations Officer of the Institute for Protein Innovation, will discuss the method, which was developed in line with the institute's mission to generate open-source antibodies against every human extracellular and secreted protein.

Dr. Love and colleagues have developed expression platforms capable of generating high-quality antigens and antibodies. These platforms are based on prior research for high-throughput production of integral membrane and other challenging proteins. Optimized transient transfection is performed via automated processes at 1 mL and 30 mL scales, and semi-automated for larger scales in HEK and CHO cells. 

Dr. Love will also discuss how the challenges associated with high throughput at larger scales are being addressed with new liquid handling platforms. 

Sponsored by