SC 7 NGS ASSAY DEVELOPMENT AND VALIDATION
MONDAY, AUGUST 14 AFTERNOON | 2:00 - 5:00 PM

Nearly 10 years after the first publication of next generation sequencing, this paradigm shifting technology has progressively migrated into the clinical diagnostic space. Multiple clinical diagnostic assays are now being routinely performed on a variety of NGS platforms, spanning from single gene to multi-gene sequencing, to genome wide analyses. Clinical laboratories implementing NGS are faced with new technical challenges augmented by the continued evolution of NGS technology, and in mastering the bioinformatics tools necessary to analyze an unprecedented sequence data volume and complexity. This Short Course will review the current technical and interpretive consideration in the application of NGS to germline and somatic disorders. Additionally, covered will be current College of American Pathologists accreditation requirements and proficiency testing for NGS.

DETAILED AGENDA:

Part One: How Multi-Gene Panel and Exome Testing are Becoming New Diagnostic Standards for Inherited Disorders

Jamie Platt, Ph.D., MB(ASCP), Managing Director, BRIDGenomics, LLC.

Part One of the Short Course will review basic advanced sequencing landscape and examine trends in assay development, technology guidelines and opportunities for supporting methodologies and technologies. The opportunities for clinical diagnostics and clinical trials will be highlighted with the specific requirements for each of these areas outlined from the diagnostic laboratory perspective. Insights into different types of clinical diagnostics laboratories will be dissected to provide participants with a more granular understanding of the NGS clinical diagnostic market. Opportunities in the changing regulatory landscape will also be discussed to provide labs and vendors with special insight into potential future solutions.

Part Two: Tackling Cancer Specimens in One Massively Parallel Sequencing Run at a Time

Jennifer J.D. Morrissette, Ph.D., FACMG, Scientific Director, Clinical Cancer Cytogenetics; Clinical Director, Center for Personalized Diagnostics, Department of Pathology, University of Pennsylvania

Part Two of the Short Course will present practical topics regarding the implementation and clinical utility of genomic sequencing for cancer diagnosis and prognosis. This discussion will focus on three topics: content, laboratory parameters and reporting and education. The first section will discuss the logistics of content (hotspot, panels, exome, whole-genome) and the implications of content decisions on testing. This will include discussion of bioinformatics, analysis and review. The second section will discuss the management of specimens with regard to DNA quality and tumor percentage and their relationship to mutation detection. The third topic will revolve around education, specifically physician education and report structure. The identification of driver mutations in a tumor can influence treatment, or can present a hurdle to the clinical team. The education and reporting section will include physician education strategies, mutation and variant categorization, allele frequency, and the incidentalome.

INSTRUCTORS:

Jamie Platt, Ph.D., MB(ASCP), Managing Director, BRIDGenomics, LLC.

Advanced sequencing technologies are highly dependent on bioinformatics tools and appropriate interpretation. In addition to applying the optimized bioinformatic algorithms with specific, validated thresholds, transforming the data into clinically useful information requires appropriate annotation. The application typically dictates the knowledge base of choice as well as the clinical interpretation. Selecting or building the appropriate bioinformatics, annotation solutions and clinical interpretation are challenges for commercial clinical labs that will be discussed within the context of Genomics, Genetics, and RNA-Seq.

Jennifer J.D. Morrissette, Ph.D., FACMG, Scientific Director, Clinical Cancer Cytogenetics; Clinical Director, Center for Personalized Diagnostics, Department of Pathology, University of Pennsylvania

Jennifer Morrissette, Ph.D. is the Scientific Director of the Clinical Cytogenetics Laboratory, the Clinical Director of the Center for Personalized Diagnostics (CPD) and an Assistant Professor at the University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA. She is certified in Clinical Molecular Diagnostics and Clinical Cytogenetics through the American Board of Medical Genetics and has been a clinical laboratory director for 10 years. Dr. Morrissette joined the University of Pennsylvania, Department of Pathology as the Scientific Director of Clinical Cancer Cytogenetics in 2010. Previous to the University of Pennsylvania, she was an Assistant Professor at Drexel University and Director of Clinical Cytogenetics and Molecular Genetic Diagnosis at St Christopher’s Hospital for Children. Dr. Morrissette was a founding member of the Center for Personalized Diagnostics, a joint initiative between the Department of Pathology and the Abramson Cancer Center.