NGS Testing Header 

Wednesday, May 6

11:00 am Conference Registration

12:15 pm Luncheon Presentation: Enriching Nucleic Acids for Next-Generation Sequencing Analyses of SNPs, CNVs, Gene Fusions and More

Joe Don Heath, Ph.D., Vice President, Market Development Diagnostics, NuGEN

The novel Single Primer Enrichment Technology (SPET) and how it differs from existing target enrichment methods will be described. Sensitive variant detection from genomic DNA derived from fresh and FFPE tissues using 344 cancer-related genes will be demonstrated as well as utilization of SPET as a rapid, cost-effective screening tool for discovery of novel fusions and detection of known fusions with a panel of 500 cancer genes implicated in fusions events.

NGS in the Clinic 

1:30 Chairperson’s Opening Remarks

Nikoletta Sidiropoulos, M.D., Medical Director, Genomic Medicine Program, University of Vermont

1:35 Using Genome Sequencing in the Clinical Setting

Jason Merker, M.D., Ph.D., Assistant Professor, Pathology, Stanford University Medical Center

Genome sequencing is increasingly being applied in clinical practice for the diagnosis of unexplained heritable disease. I will describe our experience with establishing a clinical genomics service at an academic medical center. I will then discuss the benefits and challenges identified during our initial efforts to use genome sequencing to identify the molecular etiology in patients with unexplained hereditary cancer risk.

2:00 The Realities of Implementing Clinical Genomic Testing: The Good, the Bad and the Ugly

Nikoletta Sidiropoulos, M.D., Medical Director, Genomic Medicine Program, University of Vermont

Optimizing the implementation of clinical genomic testing goes much beyond rigorous test validation. Generating genomic information and integrating it into clinical care requires collaboration between several divisions within the laboratory, clinicians, both physicians and ancillary care providers, as well as bioinformaticians, computational biologists, and information systems experts. This presentation will address key logistical elements that should be considered in an effort to optimize the clinical implementation of genomic medicine.

2:25 Laboratory-Developed Tests in the Genomic Medicine Era: Validation, Regulation and Challenges Faced by New Technologies and Clinical Applications

Andrea Ferreira-Gonzalez, Ph.D., Professor and Chair, Division of Molecular Diagnostics; Director, Molecular Diagnostics Laboratory, Department of Pathology, Virginia Commonwealth University

Laboratory-developed tests are those tests developed, validated and performed by clinical laboratories. There are standards and regulations in place for the validation of these tests before they are introduced into clinical practice. This presentation will discuss the process of validation under the current regulatory framework, and regulatory challenges posed by new technologies such as NGS and its clinical applications.

2:50 Clinical NGS: Moving from Gene Panels to Exome Sequencing

Birgit Funke, Ph.D., Assistant Professor, Pathology, MGH/Harvard Medical School; Director, Clinical Research and Development, Laboratory for Molecular Medicine, Partners HealthCare

NGS is increasingly used in the clinic, most commonly in the form of targeted gene panels that are custom tailored for specific diseases. This paradigm cannot keep up with the accelerating pace of novel discoveries, making static gene panels suboptimal for many disorders. As the quality of exome capture kits is improving, the nature of targeted panels is beginning to change from a static, stand-alone assay to a set of genes that is interrogated from an underlying exome assay.

3:20 Refreshment Break in the Exhibit Hall with Poster Viewing

4:25 Clinical Impact of NGS Multi-Gene Panels in Diagnosis and Management of Hereditary Cancer 

James M. Ford, M.D., Associate Professor, Medicine (Oncology) and Genetics, and Director, Stanford Clinical Cancer Genomics Program, Stanford University School of Medicine

4:50 Clinical NGS for Solid Tumor Testing

Rajyalakshmi Luthra, Ph.D., Director, Molecular Diagnostic Laboratory; Professor, Pathology and Laboratory Medicine, MD Anderson Cancer Center

5:15 Defining Clinical Utility for Genomic Testing

Elaine Lyon, Ph.D., Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Associate Professor, University of Utah School of Medicine; Past President, Association for Molecular Pathology

In addition to showing analytical and clinical validity, clinical laboratories are being asked to demonstrate clinical utility, or how their tests are useful in treating or managing disease. Traditional models such as large case/control studies are not feasible for rare variants identified by genomic sequencing. Alternative methods and models are needed to establish appropriate standards for molecular tests. This presentation will discuss unique challenges for molecular tests, and the need for novel solutions.

5:45 Short Course Registration

6:00-9:00 pm Dinner Short Course*

SC2: Next-Generation Sequencing as a Clinical Test 

*Separate registration required

Thursday, May 7


Agilent Technologies7:30 am Breakfast Presentation: Next Generation in Situ Hybridization (ISH) and Immunohistochemistry (IHC)

Sven Müller, Ph.D., Manager, R&D, ISH pharmDx, Dako - an Agilent Technology company

The need for solid tumor biomarkers to be confirmed in context of tissue morphology calls for routine involvement of slide based techniques like IHC and ISH. The major drawbacks of these methods relates to a qualitative readout and a slow turn-around time, respectively. Based on Dako, an Agilent Technologies Company's long term IHC and ISH expertise we are bringing these technologies to the next level, enabling us to continue being a One Stop Shop in IHC and ISH solutions for pharma partners - from early development to IVD class III kits. The symposium focuses on game changing improvements of the ISH and IHC technologies. 


NGS-Driven Clinical Trials 

8:25 Chairperson’s Remarks

Daniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core, National Cancer Institute, NIH

8:30 MSK-IMPACT: Clinical Experience with High Volume Hybrid Capture-Based Next-Generation Sequencing to Enable Personalized Oncology and Prepopulate Genetically Informed Clinical Trials

Marc Ladanyi, M.D., William Ruane Chair in Molecular Oncology, Molecular Diagnostics Service and Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center

8:55 Bringing the Power of Genomics and Next-Generation Sequencing to the NCI Clinical Trials

Daniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core, National Cancer Institute, NIH

Archer9:20 Purpose-built Targeted Sequencing Technology to Discover Gene Fusions, SNPs and CNVs in Clinically Relevant Samples

Thon de Boer, Ph.D., Technical Product Manager, ArcherDX, Inc.

Anchored Multiplex PCR (AMP™) is a target enrichment technology for NGS-based biomarker discovery.  AMP accurately detects germline and somatic mutations such as gene fusions, SNPs, indels, and copy number changes from as little as 80pg total nucleic acid.  This talk will highlight the various applications of AMP and the companion analysis software that enables detection of various gene fusions down to 0.1% simulated tumor cellularity.

9:50 Coffee Break in the Exhibit Hall with Poster Viewing

10:45 Opportunities and Challenges for NGS-Based Clinical Trials

Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity (an MPLN company)

The requirements and challenges for NGS-based diagnostics are different from those for NGS-based clinical trials. The evolving technology and regulatory landscapes present increased opportunity for utilizing NGS in clinical trials; however, a thorough understanding of workflow challenges, technical limitations and data analysis is required for optimal success. The key challenges in NGS-based clinical trials will be discussed, and opportunities around assay validation, companion diagnostics, data analysis, genomic annotation and supporting services will be highlighted.

11:10 Considerations for the Use of Comprehensive Genomic Profiling in Oncology Clinical Care and Clinical Trials

Matthew Hawryluk, Ph.D., Senior Director, Corporate and Business Development, Foundation Medicine

Oncology has engaged cancer as a disease of the genome, informed by an increased understanding of the genomic alterations that drive patient tumors. Foundation Medicine addressed the scientific, technical and practical challenges in developing a comprehensive cancer genomic profiling test based on next-generation sequencing (NGS), enabling the development of targeted therapies in the trial setting and helping appropriately identify patients in routine care. The approach advances novel treatment paradigms and accelerates progress toward truly personalized medicine.

11:35 Supporting Clinical Trials and Clinical Decision-Making through Genomic Sequencing

Jennifer J.D. Morrissette, Ph.D., Clinical Director, Center for Personalized Diagnostics, University of Pennsylvania School of Medicine

Rapid advancements in next-generation sequencing (NGS) have opened the door for unprecedented diagnostic capabilities. While these technologies make it feasible to sequence large genomic regions in very short periods of time, the overall utility is limited by the variety of targets and validation of custom assays to support immediate clinical needs. This presentation will focus on the clinical utility of genomic testing and will highlight two areas of impact. The first section will highlight the impact of genomic mutation detection on patient care and decision making. The second section will focus on the laboratory effort to support clinical trials, including the development of an NGS assay to support the chimeric antigen receptor T-cell directed therapy (CAR T) for EGFRvIII to identify appropriate patients with glioblastoma multiforma for inclusion.

12:00 pm Enjoy Lunch on Your Own

NGS Assay Development and Platforms 

1:30 Chairperson’s Opening Remarks

Seth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

1:35 Development of Clinical Sequencing Assays: Analytical Validation Approaches

Saumya Pant, Ph.D., Senior Research Investigator and Head, Sequencing Technologies, Bristol-Myers Squibb

2:00 Detection of Variants in Cardiomyopathies and Arrhythmias: Validation and Case Studies

Seth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

We detect genetic variants underlying nine myocardial phenotypes with often overlapping and/or subtle presentations. Testing is executed from a validated clinical exome (Agilent Clinical Research Exome). Data analysis and visualization are performed using a WashU developed computational suite, Clinical Genomics Workstation. I will review the design, validation and experience with this new assay.

2:25 Different Next-Generation Sequencing Platforms and Their Clinical Utility

David Smith, Ph.D., Professor, Laboratory Medicine & Pathology, Mayo Clinic

Next-generation sequencing (NGS) is a powerful technology that utilizes massively parallel sequencing to analyze many millions of DNA molecules simultaneously. The first NGS platform was developed by 454 in 2005, but this was quickly eclipsed by the Illumina sequencing platform. Today there are a number of different NGS platforms including Illumina, Ion Torrent and Pacific Biosciences. There are also numerous new NGS technologies being developed. In this presentation I will talk about the various NGS platforms and discuss their strengths and weaknesses. Then, I will discuss the clinical applications of these platforms and how these powerful technologies will totally transform the way we clinically manage cancer patients.

2:50 Close of Conference