Webinar

Optimizing Cancer Care through Strategic Selection of NGS Testing Platforms: Balancing Panel Size with DNA Input Challenges

October 24, 2024 01:00 PM US/Central

Next-generation sequencing (NGS) is a cornerstone of precision oncology, providing critical insights for the accurate diagnosis and tailored treatment of various cancers. As NGS and computational technologies continue to advance, the adoption of large, targeted panels (>500 genes) and whole-exome sequencing (WES) in molecular laboratories is on the rise. However, the success of NGS testing is fundamentally linked to the quantity and quality of input DNA. Large panels demand higher amounts of DNA, and insufficient quantities often result in Quantity Not Sufficient (QNS) outcomes, leading to delays in reporting and negatively affecting patient care.

 

Small biopsies and cytology samples, often characterized by low tumor cellularity, pose a significant challenge for successful NGS, as they typically yield lower amounts of DNA/RNA. A key advantage of in-house NGS testing is the ability to utilize platforms that accommodate low-input DNA, providing viable alternatives when comprehensive panels are not feasible.

 

In this webinar, we present comprehensive data on the success and failure rates of WES-based external testing versus in-house NGS options. We further evaluate the impact of these testing strategies on molecular-informed treatment plans and clinical outcomes. Our findings reveal that in-house NGS testing is associated with a significantly lower QNS rate. Notably, amplicon-based, small-targeted NGS panels (~50 genes) designed to work with low-input DNA offer critical therapeutic insights for patients whose samples might otherwise be deemed QNS for comprehensive testing. Furthermore, in-house large targeted panels (~500 genes) are capable of identifying actionable alterations, including targets for FDA-approved therapies and the majority of targets relevant to clinical trials in specific tumor types.

 

Our results underscore the importance of strategically selecting NGS testing approaches based on tissue availability and disease type. By incorporating flexible, alternative NGS platforms, we can enhance the success rate of NGS testing, support informed clinical decision-making and ultimately improve patient outcomes.

 

Webinar Learning Objectives

1. Analyze the advantages and limitations of different NGS approaches, including whole-exome sequencing (WES) and in-house targeted panels, in terms of their impact on genomic profiling accuracy, turnaround time, and clinical relevance.

 

2. Demonstrate how small amplicon-based NGS panels specifically designed for low DNA/RNA input from small biopsies and cytology samples can reduce the incidence of Quantity Not Sufficient (QNS) outcomes, thereby improving the success rates of genomic testing.

 

3. Develop a framework for selecting the most appropriate NGS testing platform based on tissue availability, tumor type, and clinical objectives, ensuring that patients receive the most relevant and actionable genomic data for informed treatment decisions.

 

Alexander Craig Mackinnon, MD, PhD

Professor and Director of the Division of Genomic Diagnostics & Bioinformatics for the department of Pathology, University of Alabama at Birmingham

University of Alabama at Birmingham

Dr. Alexander Craig Mackinnon, Jr is a distinguished physician-scientist in the field of pathology, currently serving as the Director of the Division of Genomic Diagnostics and Bioinformatics at the University of Alabama at Birmingham (UAB), where he is also a Professor of Pathology. Board certified in anatomical and molecular genetic pathology, he specializes in the molecular diagnostics of solid tumors. Dr. Mackinnon’s groundbreaking research in precision medicine focuses on discovering and validating therapeutic biomarkers that are revolutionizing cancer treatment. With over 80 peer-reviewed publications and 40+ invited lectures, Dr. Mackinnon is a prolific contributor to the scientific community.

Shuko Harada, MD

Professor and Director of Molecular Diagnostic Laboratory for the Department of Pathology, University of Alabama at Birmingham

Dr. Shuko Harada is a Professor in the Division of Genomic Diagnostics and Bioinformatics at UAB. Since joining UAB in 2011, Dr. Harada has driven key advancements in precision oncology, leading the Molecular Diagnostic Laboratory and the Molecular Genetic Pathology Fellowship Program. She pioneered next-generation sequencing and molecular profiling at UAB and established a multidisciplinary molecular tumor board to enhance genotype-guided cancer therapy.
 
A leader in cancer genomics and molecular diagnostics, Dr. Harada has authored over 100 peer-reviewed publications. She serves on multiple editorial boards and has held prominent roles in national societies, including President of the Association of Clinical Scientists. In 2023, she was named Clinical Scientist of the Year by the ACS.

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