GenomeWebinars

Assistant Member, Fred Hutchinson Cancer Research Center, Clinical Research Division; Assistant Professor, University of Washington, Division of Oncology

This webinar will discuss the benefits of genomically profiling the immune microenvironment of soft tissue sarcomas during neoadjuvant therapy.

Sarcomas are a group of more than 70 cancers of mesenchymal origin that together comprise approximately 1 percent of all cancers. On initial presentation, these tumors are often localized and curable. Surgery is the mainstay of therapy, but radiation and sometimes chemotherapy can also play an important role.

Unfortunately, even with state-of-the-art care, more than 50 percent of patients with large, high-grade tumors will develop advanced disease. Immunotherapy has the potential to cure many of these patients, but little is known about the changing immune microenvironment during neoadjuvant treatment for soft tissue sarcoma.

In this webinar, Seth M. Pollack of Fred Hutchinson Cancer Research Center will discuss a study that used multiple approaches to generate a molecular profile of these cancers. He will provide details of how Cofactor Genomics' Paragon assay was used to dissect the changing tumor immune microenvironment in soft tissue sarcoma during neoadjuvant therapy and will share results from the study.

Sean C. Murphy, MD, PhD, Assistant Professor, Department of Laboratory Medicine, University of Washington

This webinar will discuss how new quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) tests can accelerate the discovery and development of much-needed anti-malarial drugs and vaccines.  

Novel anti-malaria drugs and vaccines are currently evaluated using the Controlled Human Malaria Infection (CHMI) model, in which human volunteers receive a candidate drug or vaccine and are "challenged" with live Plasmodium falciparum sporozoites. Participants are then followed closely during the ensuing month, and if investigators detect the presence of malaria parasites in peripheral blood, it can indicate that the drug or vaccine was ineffective.

Historically, the gold standard test for erythrocyte stage Plasmodium infection has been microscopic examination of thick blood smears (TBS), which is analytically sensitive to 5-10 parasites per microliter of whole blood under ideal conditions. Because participants can be symptomatic prior to becoming TBS-positive, CHMI studies traditionally housed participants in a hospital ward or hotel during the potential symptomatic period. 

More recently, qPCR/RT-qPCR-based tests have improved the analytical sensitivity of infection detection by several orders of magnitude and now permit pre-symptomatic infection detection. Such tests accelerate infection detection compared to TBS and enable CHMI studies to be conducted without domiciling participants.

In this webinar, Sean Murphy of the University of Washington will discuss efforts to improve the limit of detection for Plasmodium 18S rRNA/rDNA assays to 10-20 parasites per milliliter of blood. His presentation will describe how such tests have reduced the costs, complexity, and risks of CHMI studies by accelerating infection detection and will detail external quality assurance efforts between laboratories that corroborate these diagnostic improvements. 

Recent GenomeWebinars

Director of the Laboratory for Clinical Genomics & Advanced Technology, Dartmouth-Hitchcock Medical Center & Norris Cotton Cancer Center; Professor of Pathology & Laboratory Medicine, Audrey & Theodor Geisel School of Medicine at Dartmouth

Senior Member & Chair, Department of Anatomic Pathology, Moffitt Cancer Center;  Executive Director of Esoteric Laboratory Services, Morsani Molecular Diagnostic Laboratory & Scientific Director of the Moffitt Tissue Core

 Associate Professor of Pathology, Associate Director of the Residency Program, Medical Director of Cytogenetics Laboratory & Director Georgia Esoteric & Molecular Laboratory, Augusta University

Founder & Chief Biomedical Informatics Officer, PierianDx

This webinar discussed the adoption of a commercial gene panel for tumor profiling at several leading US cancer centers.

Our expert panel — Gregory Tsongalis from Dartmouth-Hitchcock, Anthony Magliocco from Moffitt Cancer Center, Ravindra Kolhe from Augusta University, and Rakesh Nagarajan from PierianDx — specifically discuss their experiences with Illumina’s TruSight Tumor 170 targeted cancer assay.

The TST170 next-generation sequencing-based panel targets single nucleotide variants, indels, gene amplifications, gene fusions, splice variants, mRNA expression, and mRNA isoform detection found in 170 cancer-related genes and also calculates metrics such as tumor mutation burden and determines evidence for microsatellite instability.

Our panelists discuss the design of the assay, data analytics, and reasons behind their selection of the TST170 assay, and share details of how it is being utilized within their organizations. 

Sponsored by

Sr. Director of Clinical Operations, 
Rady Children’s Institute for Genomic Medicine

Scientist, Fabric Genomics

This webinar discusses the critical role of genomic interpretation software for clinical labs looking to establish comprehensive NGS testing programs. Accurate and fast software for variant calling, alignment, interpretation, and clinical reporting is an essential component of genomic medicine, with the potential to significantly impact patient outcomes and improve healthcare economics.

In this webinar, Shareef Nahas of Rady Children’s Institute for Genomic Medicine (RCIGM) presents various case studies that demonstrate how Fabric Genomics’ Opal Clinical software helps achieve accurate and rapid whole-genome interpretation of disease-causing variants in critically ill children.

RCIGM’s goal is a 24-hour turnaround time from blood sample to clinical report. Dr. Nahas discusses key interpretation and reporting capabilities needed to launch and scale clinical NGS testing, including the need for advanced computational algorithms to maximize diagnostic yield.

Our second speaker, Vanisha Mistry of Fabric Genomics, addresses best practices for adoption, deployment, and scaling of genomic data analysis platforms in the clinical lab, including automation and streamlining NGS workflows. She will review sample workflows for panels, exomes, and genomes, and will demonstrate their value to clinical labs.

Associate Director, Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center

Chief Technology Officer, Philips Genomics

This webinar presents an in-depth look at how Memorial Sloan Kettering Cancer Center has developed and implemented a next-generation sequencing panel for mutational tumor profiling of advanced cancer patients.

Michael Berger, Associate Director of the Marie-Josée and Henry R. Kravis Center for Molecular Oncology at Memorial Sloan Kettering Cancer Center, discusses the implementation of MSK-IMPACT, an NGS panel that analyzes both tumor and matched normal tissue to detect protein-coding mutations, copy number alterations, and certain promoter mutations and structural rearrangements in cancer-associated genes.

The panel, which currently covers 468 genes, has allowed a large number of patients to enroll in clinical trials of targeted treatments, according to a study published by Berger and colleagues earlier this year based on the results from sequencing around 10,000 patients. The MSKCC team found that around a third of these patients harbored actionable mutations and 11 percent of patients participated in a genomically matched clinical trial based on their results.

Since then, the MSKCC team has profiled a total of 20,000 patients with the panel. Dr. Berger discusses lessons learned from this implementation process, including:

  • Considerations in assay design
  • Challenges in large-scale implementation
  • Integration with informatics systems
  • Assessment of clinical utility
  • Opportunities for clinical, translational, and basic research

Dr. Nevenka Dimitrova discusses how the Philips IntelliSpace Genomics platform addresses the challenges of implementing molecular profiling panels at healthcare systems with integrated clinical-genomic data, up-to-date variant interpretation and seamless workflow for precision oncology.

Medical Director, Molecular Oncology Diagnostics Lab
The Ottawa Hospital

This webinar demonstrates a new approach that combines precise FFPE tumor isolation with extraction-free DNA/RNA library preparation to minimize material losses and reduce the amount of tissue input required for NGS analysis.

The need to process small quantities of solid tumor specimens is increasing as early detection strategies become more effective and less invasive biopsy strategies are adopted. Moreover, the rapidly changing landscape of molecular testing points towards a need for minimizing sample input and preservation of sample for future testing. Processing small areas of dissected tumor can be challenging as traditional manual macrodissection and purification methods include multiple steps during which material can be lost.

In this webinar, Bryan Lo, Medical Director of the Molecular Oncology Diagnostics Lab at the Ottawa Hospital, presents a new approach that combines automated tissue dissection with NGS library prepared directly from fragments of dissected tissue.

Dr. Lo discusses a study that demonstrated that gene expression profiling of pancreatic cancer and precursor lesions extracted by automated tissue dissection system yielded highly correlated data across tissue samples. Furthermore, mutation screening of dissected tissue fragments from melanoma and colorectal cancer showed high correlation between libraries prepared from an extraction-free method vs extracted DNA.

Taken together, these findings demonstrate that an automated tissue dissection approach joined with extraction-free library preparation can help efficiently process extremely small samples that are otherwise too challenging for standard NGS analysis.

Viewers of this webinar will learn the following:

  • Current challenges with isolating precise tumor areas of interest from FFPE tissue samples
  • How a high-performance, automated tissue dissection system can extract challenging tumor tissue fragments precisely and consistently
  • How to subsequently prepare NGS libraries using extraction-free methods to further reduce the risk of sample loss

Clinical Assistant Professor, Pathology, University Hospitals Cleveland Medical Center  

Associate Director, Oncology Product Management, Thermo Fisher Scientific 

This webinar discusses how next-generation sequencing (NGS) can help clinical research labs and pathologists save time, money, and samples compared to single-analyte oncology research assays.

Recent studies estimate that almost 73 percent of cancer treatments in the pipeline may need a genomic biomarker in the next few years. As the list of genomic biomarkers relevant to clinical oncology keeps growing, the ability to detect mutations across hundreds of targets in a rapid, cost-efficient fashion helps pathology research laboratories conserve samples by reducing the need for sequential, single-analyte assays. NGS panels have revolutionized the field of cancer genomics by enabling pathologists and clinical researchers to analyze mutations across multiple genes, in a single assay.

For clinical research or pathology laboratories that are considering adopting NGS in house, it’s important that the chosen solutions are compatible with challenging sample types (such as fine needle aspirates and formalin-fixed, paraffin-embedded samples), have an automated wet-lab workflow, and offer plug-and-play bioinformatics capabilities.

During this webinar, Dr. Navid Sadri of the University Hospitals Cleveland Medical Center provides an overview of why his pathology lab adopted NGS and how it is being implemented for clinical research. He provides some examples of how NGS helped identify different mutation types and provides relevant results with limited sample input and a rapid turnaround time.

Thereafter, Dr. Jody McIntyre of Thermo Fisher Scientific shows how Oncomine KnowledgeBase Reporter can help pathologists and clinical researchers link cancer variants to labels, guidelines and clinical trials, and generate an easy-to-interpret report in a few simple steps.

Assistant Professor of Medicine, Dana-Farber Cancer Institute, Harvard Medical School

Chief Technology Officer, Philips Genomics 

This webinar provides an overview of how liquid biopsies can be integrated into lung cancer care.

Genotyping of plasma cell-free DNA is rapidly changing the management approach for genotype-defined lung cancers. Widely available assays now have the ability to noninvasively identify driver mutations in cfDNA, monitor response to therapy, and characterize emerging resistance. However, such liquid biopsies also have clear limitations and existing assays are unlikely to replace tumor biopsies completely.

In this webinar, Geoffrey Oxnard of Dana-Farber Cancer Institute discusses an optimal approach for integrating liquid biopsies into lung cancer care, while also providing his outlook on how liquid biopsies may become a routine part of lung cancer treatment in the years ahead. 

Dr. Dimitrova discusses how the Philips IntelliSpace Genomics platform brings data from liquid biopsies (and other NGS tests) alongside disease histology and patient phenotype for a complete clinical picture for clinical decision making.