Next-generation sequencing has become a more affordable option in diagnosis of cancers and other genetics-based diseases. Still, technical, logistical, and ethical bottlenecks need to be addressed for this technology to become widely accepted. The Inaugural NGS-Based Assays in the Clinical Setting will address strategies for increasing specificity, developing more robust methods for analysis, and making genomic data actionable. Attendees will return to their organizations with the steps needed to manage the new treatment paradigm, from treating clinical symptoms to treating genomic pathways.
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TUESDAY, AUGUST 19
7:30 am Main Conference Registration & Morning Coffee
8:30 Chairperson’s Opening Remarks
8:40 Keynote Presentation: We Have the Technology, Now What Happens? Policy, Ethics, And Law Meet Clinical Sequencing
Robert Cook-Deegan, M.D., Research Professor, Institute for Genome Sciences & Policy, Sanford School of Public Policy, Duke University
Sequencing technologies have found their first clinical footholds in oncology, Mendelian disorder diagnostics, and prenatal screening using cell-free fetal DNA. In each area, the technology is a powerful new tool demonstrating clinical impact. In each domain, however, serious policy concerns have emerged. Controversies have flared up through patent litigation; problems in constructing pipelines for interpreting the clinical significance of sequence variants; complications in developing databases constructed for clinical rather than scientific use; privacy, confidentiality, and informed consent; inconsistent policies about who controls and has access to raw data; weak norms over data access and research transparency; and strong disagreement over what and when to convey clinical interpretations of the data to patients and families. Policy needs to catch up. Can we glimpse the road ahead through the fog?
9:10 Use of Exome Sequencing for Genetic Diagnosis: Clinical Experience and Case Examples
Wayne W. Grody, M.D., Ph.D., Professor, Medical Genetics and Molecular Pathology, Pathology & Lab Medicine, Pediatrics, and Human Genetics; Director, Molecular Diagnostic Laboratories and Clinical Genomics Center, University of California Los Angeles School of Medicine
The advent of massively parallel or next-generation DNA sequencing has finally brought into reach the long-anticipated “Thousand Dollar Genome”, or the ability to sequence an individual’s entire genome at reasonable cost. This presentation will review such aspects as clinical utility, challenges in test interpretation and genetic counseling, return of incidental findings and reimbursement, all within the context of our own experience performing clinical whole-exome sequencing at an academic medical center.
9:40 Disease Causing Potential of Variants in Untranslated Regions
Peter Nagy, Ph.D., Director, Clinical Next-Generation Sequencing Lab; Assistant Professor, Pathology and Cell Biology, Columbia University
Our laboratory offers whole-exome sequencing for clinical diagnosis of inherited disorders since the beginning of 2013. Using the Agilent SureSelect v.5 +UTRs kit allows us to capture the UTRs in addition to the coding regions. We currently do not report variants of unknown significance in the UTRs, but we are developing tools to predict the structural and functional consequences of the variants to assess their pathogenic role.
10:10 Coffee Break in the Exhibit Hall with Poster Viewing
10:55 Chairperson’s Remarks
Rajyalakshmi Luthra, Ph.D., The University of Texas MD Anderson Cancer Center
11:00 “Personalized” Breast Cancer Treatment
Peter J. Tonellato, Ph.D., Director, Laboratory for Personalized Medicine, Center for Biomedical Informatics, Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School
Essential to a future of preventive and predictive medicine is the integration of whole genome technologies into clinical and health practice. We pursue the use of WGS in breast cancer care to create a post-genome paradigm shift in health, disease prevention, and personalized medicine. These and parallel efforts, though difficult, will catalyze the adoption and widespread implementation of the post-genome competency and thereby promote the era of personalized medicine.
11:30 Development and Implementation of Clinical NGS Testing: Assay Development and Informatic Challenges
Robert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories
Currently, the major bottleneck to unlocking the full potential of this technology remains creating bio-informatic workflows that accurately identify variants within the data. During development and clinical validation of two oncology sequencing panels we were confronted with the lack of a clinical grade solution for data analysis that was adequately tested to identify hard limits of detection.
12:00 pm Incorporating NGS Assays in a Routine Molecular Oncology Laboratory
Helen Fernandes, Ph.D., Pathology & Laboratory Medicine, Weill Cornell Medical College
The presentation will address the practical processes that need to be adopted for a NGS based assay to be run in a routine clinical laboratory. Validation and implementation of NGS assays for analysis of cancer-related variants will be discussed. The presentation will focus on the pros and cons of incorporating NGS assays in molecular diagnostics laboratories.
12:30 Biomarker Discovery Through Pathway Analysis- Bringing Together Multiple Data Types for a Better Picture
Melinda Baker, Ph.D., Solution Scientist, IP & Science, Life Science, Thomson Reuters
‘Next Gen Sequencing’ (NGS) technologies produce massive amounts of data which can contain valuable information, connecting genetic variation with clinical phenotypes, and yet represent just one possible layer of biological perturbations. Here we will discuss newly released genomic analysis tools available within MetaCore™ that facilitate functional annotation of human variants and leverage pathway analysis to integrate NGS data with multiple other OMICs data types for biomarker discovery and validation.
1:00 Luncheon Presentation: Introduction to the Response Genetics Tissue of Origin Test
Debbie Corazzelli, Director, Product Marketing, Response Genetics
Response Genetics, a company focused on molecular diagnostic tests that help determine a patient's response to cancer therapy, recently introduced the FDA-cleared Response DX: Tissue of Origin Test. Looking at 2000 genes, it compares the tumor’s gene expression patterns to those of 15 known tissues, with 89% sensitivity. It is the most accurate, most published, and best validated test of its kind. The objective test results can help guide physicians in managing cancer patients.
2:00 Session Break
2:15 Chairperson’s Remarks
Seth D. Crosby, M.D., Washington University School of Medicine
2:20 Clinical Next-Generation Sequencing of Hematological Malignancies
Jennifer Morrissette, Ph.D., Scientific Director, Clinical Cytogenetics Laboratory; Clinical Director, Center for Personalized Diagnostics (CPD), University of Pennsylvania Perelman School of Medicine
The use of multi-gene testing in hematologic malignancies using NGS reliably detects somatic mutations and provides insights into prognosis and therapeutic choice. We will describe our approach to AML mutation detection, including capture of difficult to sequence regions (e.g. CEBPA and large FLT3-ITDs), and mutation profiles with respect to conventional cytogenetic findings. Finally, the utility of in clinical prognostication and treatment decisions will be discussed.
2:50 Clinical Sequencing in the Pediatric Oncology Clinic: Challenges and Opportunities
Donald “Will” Parsons, M.D., Ph.D., Assistant Professor, Pediatrics, Molecular & Human Genetics, Baylor College of Medicine, Texas Children’s Cancer Center
Current experience with the clinical application of genomic sequencing for childhood cancer patients is limited. This talk will report results of the ongoing BASIC3 study, which aims to determine the clinical impact of incorporating tumor and constitutional whole exome sequencing into the care of children with newly diagnosed solid tumors at Texas Children’s Cancer Center, with a particular focus on the diagnostic yield and limitations of WES in this setting.
3:20 Sponsored Presentation (Opportunity Available)
3:50 Refreshment Break in the Exhibit Hall with Poster Viewing
4:25 Chairperson’s Remarks
Wayne W. Grody, M.D., Ph.D., UCLA School of Medicine
4:30 Generating a Comprehensive Genomic Profile Using the High-Performance Integrated Virtual Environment (HIVE)
Raja Mazumder, Ph.D., Associate Professor, Biochemistry and Molecular Biology, The George Washington University
The High-performance Integrated Virtual Environment (HIVE) platform provides a means to store, analyze, and compute on the extra-large NGS data. However, generation of mutation profiles is only part of the story and must be followed by functional analysis of the variations if we are to derive biological and clinical meaning from the data. HIVE contains computational tools allowing for exactly this type of variation analysis and therefore serves as a vital tool in attempts to bridge whole genome analysis to disease diagnostics. Comparative analysis of mutation profiles allows better classification, and further comparison across different groups and strata can be used to create phylogenetic trees of the data set samples.
5:00 Interpretation of Clinical Genetic Data in the NGS Era
Sami S. Amr, Ph.D., Instructor, Pathology, Harvard Medical School; Director, PCPGM Research Core; Assistant Director, Lab for Molecular Medicine, Partners Center for Personalized Genetic Medicine
The rapid transition of genetic testing from Sanger sequencing to NGS technologies has paved the way for expanded gene panels as well as exome/genome sequencing. While the influx of genetic data led to increased detection rates for inherited diseases, it has also become a double-edged sword due to interpretative challenges. Standardized variant and gene assessment approaches, coupled with data sharing across diagnostic laboratories, will alleviate the interpretation bottleneck and provide more meaningful genetic results to patients.
5:30 Wine and Cheese Pairing Welcome Reception in the Exhibit Hall with Poster Viewing
6:30 Close of Day
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