GenomeWebinars

CEO, One Codex

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

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

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

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

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

Sponsored by
Thu
Jan
31
1:00 pm2019
Sponsored by
Roche

Leveraging Single-Cell Genomics to Identify Drivers of Enhanced Immunity

GenomeWebinar

Pfizer-Laubach Career Development Assistant Professor, Massachusetts Institute of Technology

This webinar highlights the use of single-cell genomics to identify distinct cell types and states associated with enhanced immunity.

Immune homeostasis requires constant regulation in order to maintain the balance between a diverse and dynamic set of cell types under normal physiological conditions. Within immune tissues, distinct cellular subsets must work together to defend against pathogenic threats, maintain tolerance, and establish memory to restore homeostasis. While surveying multiple healthy individuals enables the exploration of potential ensemble immune solutions, comparing this data against outliers of health and disease can reveal deviations that underscore diagnostic, therapeutic, and prophylactic features of enhanced function or dysfunction.

In this webinar, Alex K. Shalek of the Massachusetts Institute of Technology (MIT) will discuss his work using single-cell genomic approaches — in particular, single-cell RNA-seq — to explore the functional diversity among immune cells within and across individuals. This project aims to uncover distinct cell types and states associated with improved immunity from the molecular level.

Dr. Shalek will also expand on the emerging experimental and computational strategies for altering ensemble cellular responses through targeted intra- or extracellular induction of preferred cell types and states.

Sponsored by
Recent GenomeWebinars
Wed
Dec
12
1:00 pm2018
Sponsored by
Illumina

Precision Metagenomics to Identify Patients at Risk for Invasive Infection

GenomeWebinar

Associate Professor, Pediatric Infectious Diseases
Cincinnati Children’s Hospital

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

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

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

Sponsored by

Genetic Laboratory Director,
Repromeda Biology Park

This webinar describes a study that used two independent next-generation sequencing (NGS) platforms to gain insight into the impact of different types of aneuploidies during preimplantation genetic testing.

Preimplantation genetic testing of aneuploidies (PGT-A) enables the selection of euploid embryos in order to increase implantation rates and reduce miscarriage rates after embryo transfer. NGS platforms provide high resolution and dynamic range for detection of sub-chromosomal segmental aneuploidies and mosaicism, but the impact of these findings remains unclear.

In this webinar, Jakub Horák of Repromeda, a center for reproductive medicine and preimplantation genetic diagnosis in the Czech Republic, describes a study that compared the reproducibility of different aneuploid findings in order to gain a better understanding of their impact.

The study included 95 embryos that previously analyzed at the blastocyst stage (day 5/6) by trophectoderm biopsy and the VeriSeq™ PGS Kit from Illumina. After blastocyst re-expansion, a second trophectoderm sample of the same size was biopsied for analysis using the PG-Seq™ platform from Perkin Elmer. While detection of whole chromosomal aneuploidy was highly concordant between two samples of the same embryo (97 percent), poor reproducibility (10 percent to 50 percent) was observed for segmentals and mosaics.

These results are consistent with the assumption that the vast majority of whole chromosomal aneuploidies originate in meiosis and affect the whole embryo. In contrast, segmentals and mosaics result from genetic instability in the first mitotic divisions during early embryo development and could possibly result in a healthy livebirth when chromosomally normal cell lines are present in the developing embryo.

Dr. Horák discusses the impact of these conclusions, including the fact that these findings should be reflected in PGT-A result reporting and patient counselling.

Sponsored by

IT Director, BioFrontiers Institute, University of Colorado Boulder

Manager of IT Operations, BioFrontiers Institute, University of Colorado Boulder

Solutions Engineer, BioFrontiers Institute

This webinar provides a first-hand look at how the IT team at the University of Colorado Boulder's BioFrontiers Institute supports core facilities and research laboratories while ensuring scientific reproducibility.

Scientific reproducibility is a growing challenge in biomedicine and many other disciplines. While the biological literature is becoming more open, and data is becoming more widely shared, code written in a biomedical context is often not reproducible.

BioFrontiers IT (BIT) has approached this challenge by creating a purpose-designed IT team with scientific backgrounds and literacy. This team directly integrates into research pipelines and provides guidance and technology resources to support these efforts. BIT works with core facilities to bring reproducible computing best practices into their daily workflows using a combination of educational workshops, hackathons, and user partnerships.

In this webinar, members of the BIT team highlight real-life examples where it has deployed continuous analysis and containerization technologies to respond to the computing challenges of a modern IT group supporting core facilities and research laboratories.

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

Sponsored by

Vice President, TRAD,
Rhythm Pharmaceuticals

Founder and Chief Science Officer,
Genomenon

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

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

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

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

You will learn:

  • The importance of published genetic evidence in ensuring the success of a drug candidate
  • How to rapidly assemble a comprehensive biomarker database of this genetic evidence using data available in Mastermind
  • Why automated approaches are required for such disease-variant projects
Sponsored by
Wed
Dec
5
1:00 pm2018
Sponsored by
Agena Bioscience

Validating a Diagnostic Mass Spec Platform for a Molecular Pathology Service Lab

GenomeWebinar

Director of the Molecular Pathology Laboratory and the Program Leader for Research and Development,
Calgary Laboratory Services

This webinar will describe how a molecular pathology laboratory selected and validated a mass spectrometry-based analysis platform for diagnostic use.

Doug Demetrick, director of the Molecular Pathology Laboratory at Calgary Laboratory Services, will share his experience implementing the Agena MassArray platform in his lab.

This presentation will focus on the Agena iPLEX HS chemistry, which enables solid tumor profiling in lung, colon, melanoma, and brain samples. Dr. Demetrick will also discuss his ongoing work to enable liquid biopsy using the Agena UltraSeek chemistry.

Sponsored by
Tue
Dec
4
11:00 am2018
Sponsored by
Sophia Genetics

Clinical-Grade Exome Analysis for Complex and Unsolved Case Investigations

GenomeWebinar

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

Clinical Application Product Manager
Sophia Genetics

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

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

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

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

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

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
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
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

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
Wed
Nov
14
1:00 pm2018
Sponsored by
Streck

Quality Pillars for Building Measurement Assurance in Flow Cytometry

GenomeWebinar

Vice President, Immunology, 
Caprion Biosciences

Flow cytometry is one of the most valuable and versatile tools for multiparametric, single cell analysis. The technology has been used in research, clinical and industrial settings for more than 30 years. 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. Arguably for cell therapies, flow cytometry is the most critical tool for purity, identity and potency evaluation during the manufacturing process. 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; as well as 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 and provide specific case studies. 

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
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 provides 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 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

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
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

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

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

GenomeWebinar

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

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

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

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

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

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

Sponsored by

CEO, Girihlet

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

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

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

Sponsored by
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.

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