Close Menu

Precision Oncology Resources: Webinars

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

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

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

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

Postdoctoral Researcher,
Max Delbrück Center for Molecular Medicine 

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

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

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

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

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

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

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

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

  • Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.
  • A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution, and RNA requirements to fit the user’s needs.
  • Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.
Wed
Sep
25
12:00 pm2019
Sponsored by
HalioDx

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

Genome Webinar

Vice President of Translational Medicine
Kite, a Gilead Company

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

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

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

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

Attendees of this webinar will learn:

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

Head of Hematology and Oncology, Laboratoire Cerba

This webinar will provide an overview of how an international reference laboratory has implemented an automated next-generation sequencing workflow with custom panels for analyzing cancer samples.

Dr. Raouf Ben Abdelali, head of the Hematology and Oncology division at Cerba Laboratory, will share how his team implemented an automated protocol for Agilent's SureSelect XT HS and SureSelect XT Low Input target enrichment technology. Dr. Abdelali will review results from a wide variety of sample types (blood, fresh frozen tissue, and FFPE), sample quality, and DNA input amounts (10-200 ng).

Dr. Abdelali will discuss the design and workflow optimization of custom NGS panels for oncogenetics and onco-hematology. He will share his team's research with somatic exomes and parallel RNA-seq analysis.

Cerba provides private and hospital laboratories in more than 50 countries with a wide range of specialized clinical pathology tests in the field of hereditary genetic diseases and cancer genomics.

 

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

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

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

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

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

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

Assistant Professor, Department of Genetics,
University of Pennsylvania

Senior Product Manager
Swift Biosciences

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

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

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

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

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

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

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

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

  • Bringing genetic testing onto a technical platform for improved efficiency, analysis, and reporting.
  • The anatomy of a novel variant assessment tool that is used to classify and assess variants of uncertain significance.
  • The organization’s efforts around integrated reporting for improved diagnostic insights.
Recent GenomeWebinars

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

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

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

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

Dr. Carson discusses:

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

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

Postdoctoral Researcher, VIB-KU Leuven, Belgium

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

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

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

The main focus of this webinar is:

  • Introduction of the Tapestri Platform from Mission Bio for targeted single-cell DNA sequencing
  • Presentation of a novel custom panel covering the 300 most mutated genomic regions in ALL
  • Insights into the clonal architecture of pediatric T-ALL, lessons learned from the first 16 samples processed with this custom ALL panel
Sponsored by
Dr. Yaolin Zhou discusses Quality Improvement Model to Support Molecular Testing of Oncology Patients

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

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

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

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

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

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

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

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

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

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

R&D Manager, ID-Solutions

VP of Commercial Operations, Stilla Technologies

This webinar will outline the entire liquid biopsy workflow from cell-free DNA isolation to mutation detection by Crystal Digital PCR with the Naica System from Stilla Technologies.

Our speakers will focus on detecting EGFR, BRAF, NRAS, and KRAS mutations as well as pediatric and adult cerebral tumor classification panels.

Attendees of this webinar will:

  • Understand the liquid biopsy process for EGFR, BRAF, NRAS, and KRAS mutations;
  • Learn about the benefits of the Crystal Digital PCR platform in combination with research-use-only kits;
  • Hear why digital PCR is a particularly useful technique for the detection of mutations, therapeutic monitoring, and resistance appearance;
  • Learn about the different steps of the liquid biopsy workflow, from DNA isolation to DNA quantification and qualification and DNA genotyping, with dPCR multiplex kits

Senior Specialist Biomedical Scientist, Frontier Pathology

Specialist Biomedical Scientist, Frontier Pathology

Specialist Biomedical Scientist, Frontier Pathology

This webinar will provide a first-hand look at how a hematology/oncology lab in the UK set up and validated three molecular assays for routine in-house use.

Speakers from the Royal Sussex County Hospital (RSCH) laboratory, operated under the Frontier Pathology NHS Partnership, will share their experience implementing two assays for suspected BCR-ABL1-negative myeloproliferative neoplasms.

The RSCH lab has spent the last several years repatriating historical send-away hemato-oncology assays for JAK2 V617F and CALR exon 9. During this webinar, RSCH scientists Munyoro Guvamatanga, Anna Tarasewicz, and Rebecca Lough will share their experiences bringing these assays in-house.

The JAK2 V617F mutation assay was the first to be repatriated in 2015 and is performed using the CE-IVD marked ipsogen JAK2 RGQ PCR kit. More recently, the lab began detecting CALR exon 9 mutations using the CE-IVD marked ipsogen CALR RGQ PCR kit. The assays are performed using gDNA extracted from whole blood samples and subsequent real-time qPCR on the QIAGEN Rotor Gene Q MDx 5Plex HRM platform.

This webinar will describe the experiences and challenges associated with the setup and validation/verification of the assays in the RSCH laboratory.

Associate Professor, Biomedical Engineering, Yale University

Director, New Collaborations, Isoplexis

This webinar discusses cutting-edge single-cell approaches to discover biomarkers that could elucidate the mechanism of a variety of autoimmune disorders as well as autoimmune and inflammatory reactions to immunotherapies.  

Many therapeutics seek to address a large growing need in autoimmune and central nervous system diseases. Additionally, despite their success in addressing major challenges in refractory blood cancers, current immunotherapeutic strategies are still hampered by autoimmune-like reactions and neurotoxicity-related events. Inflammatory responses from T-cells, monocytes, and other immune cells can have detrimental effects on patients in each of these areas, but it is challenging to understand the functional profile of these immune cells, and thus how to use this type of information to predict progression of autoimmune-like responses.

Our speaker, Dr. Rong Fan of Yale University, discusses IsoPlexis’ advanced immune-based approaches in systemic lupus erythematosus and adverse events like cytokine release syndrome and neurotoxicity in cell therapy. He describes the uses of single-cell functional proteomics in determining correlates and drivers of these adverse reactions, and how these biomarkers may be used in the future to improve therapeutic development and intervention.

In addition, Jon Chen of IsoPlexis shares a case study showing that monocyte polyfunction in multiple sclerosis tracks differential responses to treatments for early diagnosis and early intervention.

This webinar will be pre-recorded. You may submit questions in advance via the registration page.

Medical Oncologist, Johns Hopkins Kimmel Cancer Center

Director of the Institute of Laboratory Medicine, German Heart Center of the Technical University

This webinar presents recent evidence that demonstrates how incorporating circulating tumor DNA (ctDNA) assessments into real-world patient management can influence patient care decisions, alter radiographic interpretations, and impact clinical outcomes.

In particular, this webinar discusses OncoBEAM a ctDNA testing method based on BEAMing (Beads, Emulsion, Amplification, Magnetics) technology developed at the Johns Hopkins University School of Medicine. OncoBEAM provides highly sensitive mutation analysis for the accurate and reliable detection of rare tumor-derived DNA present in the blood of patients with cancer.

In this webinar, Dr. Evan Lipson of Johns Hopkins shares his experience on the clinical utility of ctDNA measurements as an adjunct to radiographic imaging for monitoring disease activity in advanced melanoma patients undergoing treatment with targeted therapy or immune checkpoint inhibitors. These results have important implications for the clinical management of patients receiving immunotherapy and demonstrate the value of performing ctDNA testing for better resolution of tumor activity when performed alongside routine imaging and clinical assessments.

Next, Dr. Stefan Holdenrieder of the Technical University of Munich examines the value of KRAS-mutant ctDNA as a highly specific marker for early response prediction and treatment monitoring of advanced pancreatic cancer patients receiving chemotherapy. The discussion focuses on the potential clinical benefit of monitoring changes in ctDNA levels in response to therapy, which appear more pronounced and rapid than changes in established protein biomarkers.