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Precision Oncology Resources: Webinars

Pathologist,
Moffitt Cancer Center

This webinar will discuss how Moffitt Cancer Center has implemented a new capture-based application to accurately assess myeloid malignancies by detecting complex variants in challenging genes in a single experiment.  

Molecular profiling by next-generation sequencing (NGS) of myeloid tumors has become a routine part of disease management. One of the difficulties and limitations of NGS technology has historically been the inability to reliably detect mutations in certain GC-rich gene regions (such as the CEBPA gene) and insertions/deletions in genes such as FLT3, NPM1, and CALR. 

Many labs have circumvented these limitations by performing parallel orthogonal testing, which is redundant, costly, and inefficient. Furthermore, in late 2018, the US Food and Drug Administration approved a targeted therapy for FLT3-mutated acute myeloid leukemia, making accurate and reproducible mutation detection of paramount importance for guiding treatment.

In this webinar, Dr. Mohammad Hussaini of the Moffitt Cancer Center will discuss development of a comprehensive solution that captures 98 genes noted to be of importance in myeloid disease. In particular, he will describe:     

  • The process of evaluating and implementing this new capture-based NGS solution 
  • The accurate detection of challenging genes such as FLT3, CALR, and CEBPA 
  • The global analytical performance of this solution

Associate Scientist & Professor, Department of Urology; Vattikuti Urology Institute, Henry Ford Health System

Application Scientist, Advanced Cell Diagnostics 

Pseudogenes are a class of non-coding RNA with unknown functions. While there have been anecdotal observations pseudogene candidates with distinct functional roles, the overall genome-wide expression of pseudogenes in cancer has not reported until recently, with the help of next-generation sequencing technology.

In this webinar, Nallasivam Palanisamy of the Henry Ford Health System will discuss an effort to understand the genome-wide expression of pseudogenes across several solid cancers, which revealed a novel gene fusion involving a pseudogene in prostate cancer.

The objectives of this seminar are:

  • to present an overview of pseudogene expression in cancer
  • to discuss a method for the analysis and discovery of cancer-specific pseudogenes
  • to outline the application of RNA in situ hybridization for the analysis of pseudogenes

Professor of Pathology,
University of Pittsburgh

This webinar will discuss a study that used long-read transcriptome sequencing to explore the distribution of isoforms in colon cancer samples and their metastasis counterparts. 

The complexity of mammalian gene expression involves the combinatorial use of exons during RNA splicing. The selective splicing process generates a plethora of isoforms per gene and accounts for what is arguably the largest source of variation in transcriptome diversity and adaptability. However, the quantification of the diversity of mammalian transcriptome is impeded by the lack of accurate, quantitative, and affordable long-read isoform sequencing.

Accurate analyses of the distribution of isoforms, fusion gene isoforms, and point mutation isoforms remains a huge challenge for human malignancies. In this webinar, Jianhua Luo of the University of Pittsburgh will discuss a study that used the ability to capture transcripts from user-defined sets of genes together with synthetic long-read sequencing of full-length mRNA to characterize the long-read transcriptomes from three pairs of colon cancers and their metastasis counterparts.

Dr. Luo will share how the study demonstrated a unique pattern of RNA isoform redistribution and enrichment for specific mutated isoforms and fusions in metastatic cancer cells in comparison with their primary cancer counterparts. The isoform switching and mutation-enriched isoforms are predicted to have subtle effects on protein structure, which may differentially impact protein signal transduction and response to drug treatment.

The results demonstrate that the use of probe capture and long-read sequencing provides focus and granularity that was previously inaccessible in transcriptome analysis. Full-length transcriptome analysis may be essential for our understanding of gene expression regulation in human cancers.

Recent GenomeWebinars

VP of Research and Development, NeoGenomics

This webinar will provide a first-hand look at how a clinical lab evolved its tumor profiling workflow from a targeted panel approach toward comprehensive genomic profiling.  

Cancer is a highly complex disease and understanding the various alterations that together determine mechanisms of disease onset, progression, recurrence, and response to treatment is not trivial. These alterations, however, are not all found at the DNA level. Multimodal approaches can generate a profile of these various alterations, but this approach requires a fragmented and challenging workflow.

More recently, the field has started moving toward comprehensive genomic profiling (CGP), enabling a snapshot of the genetic makeup of the tumor at a specific timepoint. This approach provides insights beyond mutations at the nucleotide level that may provide a better understanding of the state of the disease and the various pathways that modulate its progression and response to its environment, including treatment.

In this webinar, Vincent Funari of NeoGenomics will discuss how his team has evolved its profiling approaches for both heme and solid tumors from targeted panels to more comprehensive genomic profiling.

Dr. Funari will highlight tools that enable a more streamlined path for adopting CGP, enabling operational efficiencies such as reduced overall cost while delivering high-quality data. He will also share additional insights his team gained into alterations that were previously missed due to limitations of current technologies.

Sponsored by

Co-Director, Solid Tumor and Constitutional Disease Diagnostic Laboratory,
University of Navarra

This webinar reviews how liquid biopsy can be considered as an alternative and non-invasive method to tissue biopsy for cancer molecular characterization.

Liquid biopsy enables the study of tumor-specific circulating components, including circulating tumor cells (CTCs), circulating cell-free tumor DNA (ctDNA) and RNA (ctRNA). The approach brings both great potential and new challenges to precision medicine.

This webinar highlights two key aspects of successful implementation of liquid biopsy in the laboratory: proficiency testing and interlaboratory comparison. Additionally, our speaker, Dr. Gorka Alkorta-Aranburu of University of Navarra, discusses specifics of the liquid biopsy methodology, including properties of cell-free nucleic acids and considerations for next-generation sequencing technology.

Learning objectives:

  • The benefits of liquid biopsy as a non-invasive method to better understand cancer development and treatment.
  • The advantages (and challenges) of an NGS approach to study circulating cell-free nucleic acids for clinical applications.

Clinical Lab Support Coordinator, Molecular Diagnostics Laboratory,
Sentara Healthcare Laboratory Services

Associate Chief of Clinical Pathology and Medical Director Molecular and Microbiology Laboratories,
Baystate Health

This webinar addresses how two molecular laboratories are implementing tertiary analysis software to improve their precision oncology workflows.

Solid tumor biomarker analysis by next generation sequencing (NGS) allows for better tissue stewardship and more efficient delivery of actionable results than other methodologies like single gene sequencing, but data analysis and interpretation remains a significant barrier to NGS adoption in community settings. In particular, the final tertiary analysis of NGS data is complicated by several factors, including variant-to-variant interactions, variant curation, and time to report.

Our first speaker, Dr. David Seidman of Sentara Healthcare Laboratory Servicesdiscusses how automated interpretation of NGS variants with Navify Mutation Profiler reduces the need for time-consuming and error-prone manual analysis. Software capable of automatically identifying, interpreting, and visualizing clinically relevant variant combinations promises to further decrease the manual review time necessary to account for relevant variant combinations. In a diagnostic setting, addressing variant-variant interplay in an automated fashion may also help prevent inaccurate reporting that can adversely affect the test subject.         

Our second speaker, Dr. Franklin Moore of Baystate Healthdiscusses his experiences integrating Navify Mutation Profiler into his lab's workflow, both during the evaluation phase and the clinical validation. Dr. Moore will present data on variant detection, annotation, interpretation, and tier classification compared to a manual pipeline method. He will also address, issues, challenges, and future directions.

Associate Professor,
UCSD

This webinar discusses emerging biomarkers for thyroid cancer and non-small cell lung cancer, with a particular focus on detecting gene fusions such as RET.

Our speaker, Dr. Sandip Patel of UCSD,  provides an overview of biomarker-guided therapies for thyroid cancer and NSCLC and will discuss key emerging biomarkers for these indications along with their supporting evidence.

Dr. Patel also discusses different biomarker testing approaches, practical considerations, and address challenges around fusion detection.

The webinar highlights hybrid-capture based comprehensive genomic profiling as a preferred method, along with a background and overview of this approach.