GenomeWebinars

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
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

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
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.

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. Mairead 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

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

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

Hospital Practioner, 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

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

Senior Physician, Thoracic Oncology Program, Dana-Farber Cancer Institute

General Manager,
Philips Genomics and 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
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 will discuss 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 will describe their efforts to validate the Archer VariantPlex Myeloid assay. They will 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 will 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.

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
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 will discuss 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, will share her team’s experience with integration and scale-up of the iPlex Pro Sample ID panel from Agena Bioscience. Her talk will discuss the use of the system for cost-effective sample tracking and NGS data quality assurance or germline hereditary testing.

Sponsored by

CEO, Girihlet

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

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

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

Sponsored by

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

Dijon University Hospital

Clinical Application Product Manager
Sophia Genetics

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

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) from Sophia Genetics.

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

The UK's Human Fertility and Embryology Authority calls for consumer genetic testing companies to warn customers that testing could uncover family secrets, according to the Guardian.

The New York Times reports that United Nations delegates have been discussing how to govern the genetic resources of the deep sea.

Researchers have transplanted edited cells into mice that appear to combat cocaine addiction, New Scientist reports.

In PNAS this week: analysis of proteolytic enzymes secreted by circulating tumor cells, phylogenetic study of Fv1 evolution, and more.