Precision Oncology Resources: Webinars

In this webinar, three experts in cancer testing and therapeutics will explore the pivotal role of minimal residual disease (MRD) testing in the development of oncology drugs.

Chih-Yi Hsieh, executive vice president and chief medical officer at Impact Therapeutics, Johannes Nippgen, chief medical officer, Ionova, and Zhihong Zhang, director, CTO, and general manager at Burning Rock Dx will discuss how precise MRD diagnosis can revolutionize personalized treatment strategies for cancer patients.

The speakers will discuss:

• Recent Advancements: The newest MRD detection technologies and methodologies and the latest research advancements in this field.
• Patient Care: How MRD technology enhances cancer diagnosis and guides clinical treatment, offering a non-invasive method for monitoring cancer progression and treatment response.
• Drug Development: The influence of MRD on the direction of oncology drug development and its implications for future therapies.

The transcriptional expression of tumor genomes is exceptionally complex and often driven by extensive structural variation. Key oncogenic drivers can result from gene fusions of proto-oncogenes with novel fusion partners that can be difficult to detect by DNA sequencing alone, making RNA-seq an essential step in somatic tumor profiling approaches. More recently, expressed nongenic “dark matter” in tumors has also been hypothesized as a rich source of cancer neoantigens that may direct antitumor responses. However, a current challenge in enabling routine tumor RNA-seq is the standard use of formalin-fixed paraffin-embedded (FFPE) tissue preservation that causes damage to RNA molecules and can result in poor sequencing quality.

In this webinar, Brian Piening, technical director of clinical genomics at the Providence Molecular Genomics Lab, will describe approaches for unbiased whole-transcriptome profiling in FFPE tissues and describe some key applications of this technology for answering novel questions in cancer biology.

This webinar will cover:

• Lessons learned from the implementation of an FFPE RNA sequencing pipeline.
• Challenges in RNA sequencing with FFPE samples and methods for overcoming those challenges.
• The value of whole-transcriptome sequencing for characterizing fusions.
• RNA sequencing of tumor dark matter and validation with mass spectrometry-based proteomics.
• Key considerations when implementing clinical RNA sequencing pipelines.

Learn how single-cell genomics and spatial biology are poised to advance precision medicine at PMLS Advances in Single Cell and Spatial Biology, to be held September 19 – 20, 2024, in San Diego. 

Single-cell and spatial omics technologies have provided unprecedented insights into tissue heterogeneity and biological complexity, driving new opportunities in genomic medicine. These complementary approaches have converged in recent years to create a new toolkit of methods to explore the spatial position of molecular features in a cell or tissue. 

While single-cell RNA-sequencing experiments map transcripts to individual cells, the positions of these transcripts within the tissue are not always known. And spatial transcriptomics can elucidate the location of transcripts but not always the cell that produced them. Studies using these techniques alone or in combination are producing a wealth of data to advance the fields of developmental biology, cancer, immunology, and neuroscience.

Join us to hear important insights from pioneers in single-cell and spatial omics. This two-day event, part of the 2024 Precision Medicine Leaders’ Summit series, will feature high-level discussions and ample networking opportunities with experts from key research organizations, cancer institutes, pathology labs, technology developers, and pharmaceutical executives who are driving innovation in the field and advancing the implementation of these methods into patient care.

This two-day online conference will discuss how organizations are using large-scale data in their biological data analysis and the considerations necessary to perform this research at scale. The first day will cover various genomic and multiomic data science approaches for generating biological insights. Experts will speak about using algorithms for large-scale research, data management considerations for genomic and multiomic data, and strategies for leveraging multiple data types in workflows. Our second day will shift to the ontological considerations around growing and combining datasets and how worldwide biobank initiatives keep their data secure while distributing it to a global community. Learn about the latest data models for working with large-scale datasets and creating secure ecosystems for multimodal data.

In this webinar, Rui Chen, director of the Center of Single Cell Omics at Baylor College of Medicine, will report on the generation of a comprehensive atlas of full-length transcript isoforms in the mouse retina at the single-cell level using long-read single-cell RNA Sequencing. Chen’s team profiled approximately 30,000 mouse retina cells using a combination of 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore long reads.

Important findings:

• Results in gene expression and cell annotation between long-read and short-read datasets were comparable. The lab’s results indicate that single-cell long-read RNA sequencing alone would be sufficient to capture the information.

• Leveraging long-read scRNA-seq, the lab detected a total of 44,325 transcript isoforms, among which over 16,000 are novel. Furthermore, the team pinpointed 7,383 isoforms exclusive to specific cell classes, a considerable portion of which were novel.

• Isoform usage patterns varied among different cell classes and subclasses.

• A total of 1,055 intra-chromosomal gene fusions were detected within the mouse retina.

The diagnostic process for hematologic malignancies can be complex and time consuming; it includes morphological analysis of bone marrow and peripheral blood, immunohistochemistry, flow cytometry, cytogenetics and, under certain circumstances, additional testing.

Starting with morphology, flow cytometry, and cytogenetics can help reduce unnecessary or duplicative testing that may not be covered by insurance. Additional testing can then be performed if recommended by guidelines or if results are inconclusive. This workflow requires close collaboration between clinicians and laboratory staff but enables more timely and efficient diagnostic and prognostic information to help guide treatment decisions.

In this webinar, Girish Kunapareddy, clinical assistant professor of medicine at Indiana University School of Medicine, and Stephanie McAlhany, medical director at Labcorp Oncology’s Brentwood Laboratory, will review a case and discuss how clinicians and laboratory staff can work together to alleviate complexities in the diagnostic process for hematologic malignancies.

With over 1,500 clinical trials incorporating liquid biopsy testing, the use of ctDNA monitoring is rapidly expanding. Initially used to identify acquired resistance variants, ctDNA is now crucial for evaluating residual disease and assessing molecular responses to therapies, such as antibody-drug conjugates, or ADCs. This allows for quick decision-making in translational research.

In this webinar, Jonathan Beer, senior director of diagnostic sciences at Bristol Myers Squibb, will share the pharmaceutical sector’s perspective on the multifaceted applications of ctDNA. Learn how ctDNA aids in selecting therapy based on specific biomarkers and offers early insights into molecular response.

Christine Petersen, director of business development at Foundation Medicine, will present new data from the FoundationOne Monitor ctDNA monitoring assay and its potential for enabling researchers and drug developers to gain insights using ctDNA throughout clinical programs.¹ She will also report on how biopharma partners have used FoundationOne Monitor to optimize dose selection for new therapies in early-phase trials and add value beyond standard pharmacodynamic analysis.

The speakers will:

• Explore ctDNA monitoring applications in biopharmaceutical drug development.
• Examine case studies highlighting ctDNA's impact in clinical trials.
• Introduce FoundationOne Monitor, a tissue-naive test for ctDNA monitoring
• Reveal how ctDNA can enhance drug development strategies.  

1. For Investigational Use Only. The performance characteristics of this product have not been established.

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Advances in biomarker testing, analytical methods, and real-world datasets (RWD) that include biomarker and clinical data are rapidly enhancing precision oncology, enabling both forward and reverse translation and allowing for more effective patient-specific treatments. These innovations play a crucial role in drug development, as well as clinical, payor and regulatory decision making. However, it's crucial to consider the strengths and limitations of different approaches and datasets when designing analyses and interpreting precision oncology data.

In this webinar, Milan Radovich, chief scientific officer at Caris Life Sciences, Professor Charu Aggarwal, from the University of Pennsylvania, and Neal Meropol, vice president of research oncology at Flatiron Health, will explore the evolving state of precision oncology research and the pivotal role that high-quality linked clinical and multiomic RWD plays in accelerating all stages of drug development to maximize the success of novel therapeutics. The webinar will be moderated by Flatiron’s Kristin Zimmerman Savill, director of scientific engagement for precision oncology.

The speakers will discuss:

• The rapidly evolving state of precision oncology research.
• Key considerations for different methodological approaches and datasets when designing or interpreting data from precision oncology research.
• Case studies highlighting how RWD can be used more effectively in precision oncology research to drive the development of novel and effective therapies, guide clinical, payor and regulatory decision-making, and improve patient outcomes.

This event, developed with guidance from the editorial team of Precision Oncology News, will focus on the rapidly evolving field of precision oncology, including new diagnostic and therapeutic modalities, regulatory and reimbursement trends, and implementation challenges.

PMLS Precision Oncology and Diagnostics 2024 will bring together key stakeholders to discuss strategies and best practices for implementing molecularly guided cancer care. Thought leaders from pharmaceutical and biotech firms, leading cancer centers, and the research community will share real-world experiences in delivering precision oncology to patient populations.

Anyone tracking the opportunities and challenges associated with individualized cancer therapy will want to attend this event, including oncologists, pathologists, health system executives, regulatory and reimbursement experts, clinical researchers, and pharmaceutical/biotech executives.

overview

This event, part of the Precision Medicine Leaders’ Summit conference series and developed in partnership with the University of Pennsylvania Institute for Biomedical Informatics, took place June 25 - 26, 2024

The conference explored how multiomics methods are advancing precision medicine in a range of human disease areas.

Recent advances in multiomic approaches — including genomics, transcriptomics, epigenomics, proteomics, and metabolomics — enable a more comprehensive picture of disease biology. This promises to accelerate the development of precision medicine, but also presents challenges for researchers, clinicians, and health systems struggling to integrate disparate data sources into a cohesive clinical strategy.

Multiomics in Precision Medicine 2024 highlighted best practices, trends, and strategies from experts who are successfully implementing a range of omics approaches to advance molecularly informed medicine.