This session will comprehensively explore the latest advancements in structural variant (SV) analysis for clinical diagnostic workflow, specifically focusing on the emerging data pertaining to long-read sequencing. The speakers will review the currently available technologies for SV detection, highlighting the advantages and challenges, delve into the clinical applications of long-read sequencing and discuss bioinformatics infrastructure essential for supporting these workflows. Attendees will gain understanding of current and emerging approaches to SV analysis and prepare them to integrate these technologies effectively in clinical practice. 

Learning Objectives

1. Provide an overview of the currently available technologies for SV detection, and compare their clinical utility, advantages, and limitations to guide the laboratories in selecting the most suitable technology for implementation.  
2. Explore the utility of long-read sequencing technologies for clinical SV detection highlighting the advantages and challenges. 
3. Identify essential bioinformatics infrastructure and tools required for long-read sequencing implementation, computational workflow, and robust data integration. 

The rapid growth of genomic data has revolutionized cancer research and clinical diagnostics. Central to this progress is the role of variant interpretation databases, such as Clinical Interpretation of Variants in Cancer (CIViC), Variant Interpretation for Cancer Consortium (VICC), and ClinVar, in facilitating data sharing. This session will provide an overview of these databases, and highlight the work of VICC and their efforts to standardize the curation, representation, and interpretation of clinically relevant evidence associated with genomic variation in cancers.

Learning Objectives

1. Review the cancer variant interpretation databases
2. Demonstrate how to use the VICC Meta-Knowledgebase
3. Summarize the proceedings of the VICC/CGC/CIViC/ClinGen Cancer Variant Curation and Coding Unconference Agenda

This session will provide a comprehensive overview of bioinformatics workflows for processing, analyzing, and visualizing cancer genome data to support clinical decision-making. Attendees will gain insights into best practices for interpreting and classifying somatic and germline variants, with an emphasis on integrating data with established databases and clinical guidelines. The discussion will highlight how bioinformatics tools enable the identification of diagnostic, prognostic, and therapeutic biomarkers, empowering clinicians and researchers to drive precision oncology forward.

Learning Objectives

1. Learn about end-to-end workflows for processing, analyzing, and visualizing cancer genome data to support clinical decision-making.
2. Explore best practices for interpreting and classifying somatic and germline variants in cancer genomes, including integration with databases and guidelines.
3. Learn how bioinformatics facilitates the identification of diagnostic, prognostic, and therapeutic biomarkers in cancer.

This session will provide an overview of the federal regulations governing molecular diagnostic testing and the complex issue of gene patenting. Participants will learn about the regulatory landscape that ensures the safety, effectiveness, and ethical application of molecular diagnostic tests in clinical settings. The session will also delve into the legal complexities surrounding gene patenting, including how intellectual property laws affect the development and accessibility of genetic testing technologies. Key topics will include the federal regulation of molecular diagnostic testing and the implications of the U.S. Supreme Court’s decision in the "Association for Molecular Pathology v. Myriad Genetics" case on gene patenting.

Learning Objectives

1. Identify key federal requirements for the approval and regulation of molecular diagnostic tests.
2. Assess the balance between regulatory oversight and the promotion of innovation in the molecular diagnostics and biotechnology sectors, considering both safety and commercial interests.
3. Examine the history and current legal status of gene patenting in the U.S., including the impact of the Myriad Genetics decision and the role of patent laws in the development of genetic testing.
4. Explore the ethical issues surrounding gene patents, including concerns related to accessibility, innovation, and healthcare equity, and how federal regulations address these concerns.

Integrating molecular genetics and cytogenetics laboratories offers significant advantages, including a more comprehensive understanding of genetic abnormalities, improved accuracy in molecular diagnosis, and reduced redundant testing. This integration enables a cost-efficient diagnostic workflow while enhancing molecular classification, risk stratification, and treatment planning. However, challenges such as standardizing methodologies, cross-training personnel, and ensuring cost-effective consolidation, as well as the implementation or de-implementation of tests and testing platforms, must be addressed. Despite these concerns, the integration of cytogenetics and molecular genetics laboratories is pivotal for advancing precision medicine and improving patient care. In this session, experts will share their insights on integrating molecular genetics and cytogenetics laboratories, as well as their experiences and considerations when transitioning from traditionally separated molecular and cytogenetic laboratory efforts to the integrated molecular genetics and cytogenetics testing strategy. 

Learning Objectives

1. Understand the capabilities and limitations of cytogenetics and widely used molecular genetics testing approaches from a technical perspective, and their roles in diagnostic applications.
2. Explore the benefits of integrating these laboratories, including enhanced accuracy, efficiency, and improved patient outcomes.
3. Identify key challenges in the integration process, including technical, financial, and personnel training aspects.
4. Develop strategic approaches to harmonize workflows, ensure a seamless transition, and implement best practices for laboratory integration.

This workshop will explore different perspectives on balancing professional and personal fulfillment in various career paths in clinical genomic diagnostics. The speakers will discuss negotiation of protected research time while in clinical service, staying connected while working remotely, etc. The attendees will learn about optional career paths in clinical diagnostics and about ways to enhance work-life balance and achieve enhanced satisfaction in their careers.

Learning Objectives:

1. Identify the key differences between academic and non-academic clinical pathways by understanding the unique roles, expectations, and career trajectories.
2. Identify strategies to stay motivated and focused on long-term career and personal happiness in your career path.
3. Gain insight into making smooth transitions between different stages of an academic or non-academic career.
4. Explore strategies for managing time and stress to maintain personal well-being while pursuing professional success in academic medicine.

This workshop will introduce key web tools and databases for identifying recurrent biomarkers in cancer genomes. The maintainers of these resources will demonstrate essential features and discuss their applications in research and clinical settings. Attendees will gain hands-on experience exploring these tools and engaging directly with the experts who build and maintain them.

Learning Objectives:

1. Discover resources for retrieving recurrent cancer genetic/genomic biomarker data.
2. Explore interfaces to publicly available cancer genetic/genomic biomarker databases with the resource creators.
3. Understand strengths and limitations of recurrent cancer genetic/genomic biomarker datasets.
4. Consider strategies for applying recurrent cancer genetic/genomic biomarkers in variant interpretation.