Cambridge Healthtech Institute’s Third Annual
Clinical NGS Assays: Technologies and Validation
Establishing Next-Generation Sequencing as the Standard of Care
August 15-16, 2017 | Grand Hyatt Washington | Washington, DC
With applications spanning oncology, genomics, and infectious diseases, next-generation sequencing (NGS) has become an integral part of the diagnostics landscape. Still, there is work to be done to establish these tools as the standard of care. The Third Annual Clinical NGS Assays: Technologies and Validation will emphasize assay validation, establishing standards, and platform evaluation. Additional focus will be given to clinical use cases of molecular oncology tools, challenges in pathogen sequencing, and advances in inherited disease diagnostics. Overall, this event will address the needs of both researchers and clinicians while exploring strategies to increase collaboration for improved patient outcomes.
Final Agenda
Recommended Short Course(s)*
SC1: NGS Diagnostics: Technology, Regulation and Reimbursement
SC16: NGS for Infectious Disease Diagnostics
*Separate registration required
TUESDAY, AUGUST 15
7:30 am Main Conference Registration & Morning Coffee
8:30 Chairperson’s Opening Remarks
Larissa V. Furtado, M.D., Medical Director, Molecular Oncology, ARUP Laboratories; Assistant Professor, Pathology University of Utah
8:40 Using Specimens with Limited Material for Detection of Variants in Lung Cancer
Helen Fernandes, Ph.D., Associate Professor, Personalized Genomic Medicine, Pathology and Cell Biology, Columbia University Medical Center
Minimally invasive diagnostic procedures, such as needle core biopsies or fine needle aspiration (FNA) often provide adequate material for molecular analyses. One of the greatest advantages of cytology samples in molecular testing is that they are often collected in non–formalin-based fixatives, and provide superior quality of nucleic acids that is more amenable to accurate interpretation of genomic sequence data. Such interventional biopsies can be subject to the challenges of neoplastic cellularity and tumor heterogeneity. Advances in precision oncology are trending towards the interrogation of limiting amounts of genomic material to guide clinical and therapeutic decisions. This presentation will address the current challenges in using small and degraded samples for genomic testing.
9:10 Development and Validation of Clinical Oncology Next Generation Sequencing
Larissa V. Furtado, M.D., Medical Director, Molecular Oncology, ARUP Laboratories; Assistant Professor, Pathology University of Utah
Developing next generation sequencing (NGS) assays for clinical oncology can be a significant challenge for clinical laboratories. In addition to substantial investments in infrastructure and personnel, the nature of cancer specimens and the complexities of NGS raise many pitfalls for assay development and validation in the clinical setting. This talk will provide a practical overview of validation approaches and considerations for clinical oncology NGS.
9:40 Molecular Insights from Exome and Transcriptome Sequencing in Pediatric Cancer
Susan J. Hsiao, M.D., Ph.D., Assistant Professor, Pathology and Cell Biology, Columbia University Medical Center
Exome and transcriptome sequencing has shown great promise in providing molecular profiles that can be used to guide patient management and therapy. Incorporating sequencing into clinical practice can be challenging, but such integration yields not only actionable but also clinically impactful results in a significant percentage of cases.
10:10 Coffee Break in the Exhibit Hall with Poster Viewing
10:55 Chairperson’s Remarks
Helen Fernandes, Ph.D., Associate Professor, Personalized Genomic Medicine, Pathology and Cell Biology, Columbia University Medical Center
11:00 The SPOT/Dx Diagnostic Quality Assurance Pilot Study
John D. Pfeifer, M.D., Ph.D., Vice Chair for Clinical Affairs, Pathology, Washington University School of Medicine
In the field of clinical next generation sequencing (NGS) there is a need to demonstrate that equivalent results are produced by different laboratory tests performed by different laboratories. The SPOT/Dx Diagnostic Quality Assurance Pilot Study is a multi-stakeholder initiative designed to address this concern. Specifically, the pilot study will develop reference samples that will be used to evaluate the performance of LDTs to selected CDx for targeted cancer therapy.
11:30 Improving the Definitive Diagnosis Rate: Clinical Application of Whole Genome Sequencing
Liz Worthey, Ph.D., Faculty Investigator, Director, Software Development and Informatics, HudsonAlpha Institute for Biotechnology
Application of genome sequencing in a clinical setting has altered how molecular diagnoses are obtained, uncovering novel loci and tripling the diagnostic success rate in patients with rare genetic disease. With initial frameworks in place the focus is on result oriented refinement of tools, algorithms, and methods to reduce the time and resources required to obtain definitive diagnoses. I will discuss advances in our methodology and applications, providing examples as to how refining the process has resulted in unexpected diagnoses, novel insights, and better clinical decision making.
12:00 Panel Discussion with Session Speakers
12:30 Accelerating Liquid Biopsy Assay Development with the Most Patient-like ctDNA Reference Materials
Russell Garlick, CSO, SeraCare Life Sciences
As liquid biopsy assays continue to revolutionize cancer diagnostics, there is a desperate need for reference materials that mimic native ctDNA in terms of relevant somatic mutations, fragment size distribution, library yield, and library complexity. In response, SeraCare has developed ground-breaking technology to address this critical need. We will present data from early access customers that illustrate how these materials are helping accelerate development and implementation of more robust ctDNA assays.
1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:30 Refreshment and Cookie Break in the Exhibit Hall with Poster Viewing
2:00 Chairperson’s Remarks
John D. Pfeifer, M.D., Ph.D., Vice Chair for Clinical Affairs, Pathology, Washington University School of Medicine
2:05 Automating the Process of Sample Preparation
Joshua T. Smith, Ph.D., Research Staff Member, Translational Systems Biology and Nanobiotechnology, IBM T.J. Watson Research Center
We recently used nanoscale deterministic lateral displacement (nanoDLD) technology for on-chip size separation of exosomes and DNA, a system with sensitivity sufficient to interrogate individual exosomes and DNA molecules even in samples with low concentrations of analyte. In this talk, I will showcase our latest developments in automating the processes of isolation, enrichment and purification of analytes from native sample for downstream analysis.
2:35 Next-Generation Sequencing Approaches to Aid in Diagnosis Clarification: Improving Insight and Adding Value
Eric Konnick, M.D., MS, Acting Assistant Professor, Laboratory Medicine, University of Washington
Clinical germline testing for cancer-risk syndromes frequently does not identify mutations that can be used to guide clinical decisions. Using data from NGS platforms acquired from neoplastic tissues, in combination with germline data, many patients can be provided with relevant information to help guide cancer screening and treatment of individual patients and their extended family. Such approaches offer value to patients and are likely to become standard of care.
3:05 Error-Corrected Ultra-Deep Sequencing for Clinical Applications
Eric Duncavage, M.D., Assistant Professor, Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University School of Medicine in St. Louis
A major unmet clinical need is the ability to monitor patient tumor burden or measurable residual disease (MRD) in response to treatment. For certain tumor types the presence detectable tumor burden after treatment is a poor prognostic indicator. Tumor clearance or MRD monitoring could also serve as a more rapid surrogate endpoint for clinical trials. This talk will focus on the use of newer error corrected sequencing methods to detect MRD in cancer patients.
3:35 Molecular Tagged NGS Libraries for Detection of Rare Variants and a SMARTer Approach to Gene Fusion Identification
Rachel N. Fish, Ph.D., R&D Scientist, Takara Bio USA
Identification of rare mutations and gene fusions is key to understanding disease. Here we introduce the ThruPLEX Tag-seq technology which uses unique molecular tags to enable detection of low-frequency variants at high sensitivity and specificity. We also present a new approach leveraging the SMARTer 5’-RACE technology to detect gene fusions.
3:40 NEBNext Direct: Pre-designed Gene Content Enables Rapid Deployment of High-Quality Customized Enrichment Panels
Andrew Barry, Product Marketing Manager, Target Enrichment, New England Biolabs, Inc.
NEBNext Direct target enrichment overcomes challenges translational researchers face in selectively enriching genomic targets. Allowing enrichment of a single gene up to panels comprised of hundreds of genes without compromising performance, NEBNext Direct provides the specificity and coverage uniformity to maximize sequencing efficiency in a single-day, easy to use protocol.
4:05 Refreshment Break in the Exhibit Hall with Poster Viewing
4:50 PANEL DISCUSSION: Early Detection with Liquid Biopsy: Pipe Dream or Possibility?
Moderator: Lynn R. Sorbara, Ph.D., Program Director, Cancer Biomarker Research Group, National Cancer Institute
- Challenges
- Gaps
- Wish list
- Can existing technologies be adapted?
Panelists:
Daniel Danila, M.D., Genitourinary Oncology Service, Medicine, Memorial Sloan-Kettering Cancer Center
Utkan Demirci, Ph.D., Associate Professor, Radiology, Stanford University
James Hicks, Ph.D., Professor, Biological Sciences, University of Sothern California
5:50 Wine & Cheese Pairing Welcome Reception in the Exhibit Hall with Poster Viewing
6:50 Close of Day
WEDNESDAY, AUGUST 16
7:15 am Registration
7:30 Problem-Solving Breakout Discussions with Continental Breakfast
Utilizing Next-Generation Sequencing Techniques for Precision Oncology
Moderator: Helen Fernandes, Ph.D., Associate Professor, Personalized Genomic Medicine, Pathology and Cell Biology, Columbia University Medical Center
- Choosing the right assay for your patients
- Selecting and Classifying clinically relevant variants
- Current and future challenges
Analysis of Microbiome Data
Moderator: Patrick Gillevet, Ph.D., Professor and Director, Microbiome Analysis Center, George Mason University
- Which clustering algorithm to use… to cluster or not to cluster?
- Which Taxonomic classification system to use?
- Data storage requirements?
- Should we move to analysis on the cloud… performance and security issues?
- Machine Learning issues?
8:25 Chairperson’s Opening Remarks
Jonathan Jacobs, Ph.D., Senior Advisor, Global Health and Surveillance, MRIGlobal
8:30 Validating Metagenomic Next-Generation Sequencing for Clinical Care: The Clinical Microbiology Perspective
Patricia Simner, Ph.D., D(ABMM), Director, Bacteriology and Parasitology, Division of Medical Microbiology, John's Hopkins
As more and more peer-reviewed literature is released on the successful application of metagenomic next-generation sequencing for infectious disease diagnoses – the more pressure is applied to Clinical Microbiology Laboratories to bring in and validate the technology for clinical care. This presentation will discuss the challenges from a Clinical Microbiology Laboratory perspective when adopting NGS and will walk through the various decision points when validating NGS for clinical care.
9:00 Universal Pathogen Detection by Next-Generation Sequencing in Routine Diagnostic Practice
Robert Schlaberg, M.D., MPH, Medical Director, ARUP Laboratories, Assistant Professor of Pathology, The University of Utah
Routine tests often fail to provide etiologic diagnoses in common diseases like pneumonia and encephalitis/meningitis. Early etiologic diagnosis is critical for effective treatment and reduces morbidity and mortality. NGS strategies can provide universal pathogen detection and improved diagnostic yield. However, complex workflows and long turnaround times have hindered adoption. We have developed and validated tools for rapid NGS-based universal pathogen detection providing results within 48 hours.
9:30 Genotypic Antiviral Resistance Testing by Next-Generation Sequencing
Benjamin Pinsky, M.D., Ph.D., Assistant Professor, Departments of Pathology and Medicine, Stanford University School of Medicine; Medical Director, Clinical Virology Laboratory, Stanford Health Care and Stanford Children’s Health
The emergence of drug resistance is an important factor in the management of clinically significant viral infections, particularly HIV-1. Genotypic drug resistance testing by conventional Sanger sequencing has limited sensitivity for low-frequency drug resistance mutations, whereas NGS methodologies allow the detection of minority variants associated with virological failure. This presentation will focus on the clinical application of NGS to genotypic antiviral resistance testing.
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10:00 Nucleic Acid Technologies to Empower Clinical Diagnostics: from Sample Integrity to Multiplex PCR
Mirna Jarosz, Director, NGS Scientific Applications, Integrated DNA Technologies
The advancement of molecular diagnostics often relies on increasingly complex nucleic acids for key assay components. Here, we present three applications of new nucleic acid technologies: an allele-specific, quantitative, PCR assay using RNase H2-dependent PCR (rhPCR) and a universal reporter system; a highly multiplexed rhPCR method to rapidly create Next Generation Sequencing (NGS) libraries for validating sample integrity; and using dual-matched NGS adaptors to resolve index hopping that could otherwise lead to sample crosstalk.
10:30 Coffee Break in the Exhibit Hall with Poster Viewing
1:05 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:35 Ice Cream and Cookie Break in the Exhibit Hall with Poster Viewing
1:35 Close of Clinical NGSAssays