Molecular Diagnostics

Molecular diagnostics is leading disruptive innovation in healthcare by the introduction of many tools that are having a profound impact on healthcare delivery. These include next-generation sequencing, wearable sensors, liquid biopsies, direct-to-consumer testing, point-of-care assays, and early cancer detection. Join industry leaders at the Molecular Diagnostics event to discuss recent developments and decipher how changes in regulation, reimbursement, and implementation guidelines will impact progress in new markets created by innovations in this technology.

Scientific Advisory Board

Edward Abrahams, Ph.D., President, Personalized Medicine Coalition

Daniel H. Farkas, Ph.D., HCLD, Section Head, Molecular Pathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic

Andrew C. Fish, J.D., Chief Strategy Officer, AdvaMed; Executive Director, AdvaMedDx

Eric van Gieson, Ph.D., Program Manager, Program Manager, Defense Advanced Research Projects Agency (DARPA) Biological Technologies Office

 

Monday, February 12

10:30 am Conference Program Registration Open

NEW CLINICAL PRACTICE GUIDELINES FOR NGS-GUIDED ONCOLOGY

11:50 Chairperson’s Opening Remarks

Maria E. Arcila, M.D., Pathologist and Director, Diagnostic Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center (AMP Member)

12:00 pm Role of Practice Guidelines in NGS Oncology Testing

Maria E. Arcila, M.D., Pathologist and Director, Diagnostic Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center (AMP Member)

Providing clinically relevant test results using next-generation sequencing methodologies is a complex process, requiring both analytical rigor and the expertise of molecular medical professionals. The Association for Molecular Pathology has convened and led a series of multidisciplinary subject matter expert working groups in collaboration with ACMG, AMIA, ASCO, and CAP to provide evidence-based NGS best practice guidelines. This trio of peer-reviewed publications provides a foundation for NGS testing procedures that spans the length of the process – from sample acceptance to production of a standardized report. By establishing guidance for laboratories and clinicians, professional organization driven practice guidelines work to improve patient care.

12:15 Best Practices for Validation of Clinical Next-Generation Sequencing Bioinformatics Pipelines

Somak Roy, M.D., Assistant Professor, University of Pittsburgh Medical Center (AMP Informatics Subdivision Representative to the AMP 2018 Program Committee; Member)

Bioinformatics pipelines are an integral component of next-generation sequencing (NGS) assay. However, there is significant variability in how bioinformatics pipelines are validated in the global molecular genetics and pathology community in the absence of published guidelines. To address this, the Association of Molecular Pathology (AMP) with liaison representation from the College of American Pathologists (CAP) and the American Medical Informatics Association (AMIA) have developed a set of best practice consensus recommendations for the validation of clinical NGS bioinformatics pipelines.

12:30 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

Marina N. Nikiforova, M.D., FCAP, Professor, Pathology; Director, Molecular & Genomic Pathology Laboratory, Pathology, University of Pittsburgh Medical Center (AMP Member)

Sequence variants detected by NGS are used to assist with diagnosis, prognostication and treatment of patients with cancer. The Association for Molecular Pathology, with liaison representation from the American Society of Clinical Oncology, and College of American Pathologists, and American College of Medical Genetics and Genomics (ACMG) have created consensus guidelines for annotation, interpretation, and reporting of somatic variants in cancer. The guideline describes a system for evidence-based variant categorization and the process of variant annotation, classification, and reporting.

12:45 PANEL DISCUSSION: New Clinical Practice Guideline Publications to be Discussed

  • Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels. A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. Published in the May 2017 Issue of the Journal of Molecular Diagnostics.
  • Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. Published in the January 2017 issue of The Journal of Molecular Diagnostics.
  • AMP Bioinformatics Pipeline Validation Guidelines Working Group Manuscript (submitted for publication)

1:00 Session Break

DNA Software1:10 Luncheon Presentation I: Large Scale Multiplex PCR Panel Design with >95% Success in Hours, Not Months

John SantaLucia, Ph.D., co-founder and CEO, DNA Software

We aim to solve the problem of multiplex PCR design by a three-pronged approach: 1. improved understanding of the mechanism of PCR and the causes of artifacts, 2. improved algorithms for predicting 2 structure and mis-hybridization, and 3. implementation of cloud to address large sequence databases. These approaches vastly improve the success of fully automated multiplex PCR design with larger plex sizes. This enables applications such as targeted enrichment for NGS and infectious disease molecular diagnostics.

 

 1:40 Luncheon Presentation II (Sponsorship Opportunity Available)

2:10 Session Break

REGULATORY CHALLENGES AND OUTLOOK

2:30 Chairperson’s Remarks

Andrew C. Fish, J.D., Chief Strategy Officer, AdvaMed; Executive Director, AdvaMedDx

2:40 Future of Molecular Diagnostics Regulation

Paul Radensky, M.D., J.D., Partner, Health Industry Advisory Practice Group,

McDermott Will & Emery LLP

Molecular diagnostics are regulated by CLIA (LDTs) and FDA (IVD kits).Companion diagnostics are regulated as medical devices whether offered as LDTs or IVDs. FDA has indicated its intent to regulate most LDTs as medical devices, but FDA’s plans have been delayed. What is the best regulatory approach that balances protecting public health with goal of incentivizing innovation to improve patient care and realize the benefits of precision medicine?

3:10 Innovative FDA Approval Process - 23andMe’s Experience

Kathy Hibbs, J.D., Chief Legal and Regulatory Officer, 23andme

In 2013, FDA issued a warning letter toz 23andMe, requiring it to cease sales ofits direct to consumer genetic health reports until it obtained FDA’s pre-market authorization. In 2015, 23andMe obtained the first FDA authorization for an over-the-counter genetic test and class II exemption for providing autosomal carrier status information directly to consumers. In 2017, 23andMe obtained the second FDA authorization for over-the-counter genetic information and a further class II exemption enabling it to provide information on genetic health risks directly to consumers.

3:40 PANEL DISCUSSION: Regulatory Challenges for Novel Diagnostics

  • Regulatory considerations and outlook for test developers
  • Status of Congress’ efforts to develop legislation reforming diagnostics oversight, including LDTs
  • Latest developments at FDA
  • How novel technologies and tests are challenging FDA
  • Lessons learned on to work effectively with FDA

4:10 Real-World Evidence for Diagnostics

Shivang Doshi Director Boston Healthcare Associates

More real-world evidence is needed to support adoption and clinical utility definitions for advanced diagnostics. Different types of data sources and the various purposes they fulfill, and system design for on-going evidence collection that supports organic information collection on the impact of diagnostic innovation on clinical practice will be examined.

4:25 Closing the Gap: Commercialization and Coverage for Novel Diagnostics

Kyle Fetter, Executive Vice President & General Manager, Diagnostic Services, MDx Support Services, XIFIN, Inc.

Early stage diagnostic and wearable diagnostic device companies face greater hurdles to commercialization and reimbursement than ever before. The combination of clinical, market adoption, and reimbursement hurdles make it imperative to synch up all efforts within an organization for diagnostic providers from early-stage product development to commercialization and payor contracting.

4:40 Refreshment Break and Transition to Plenary Session

5:00 Plenary Keynote Session (click here for more details)

 

Precision for Medicine

6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing

7:30 Close of Day

Tuesday, February 13

7:30 am Registration Open and Morning Coffee

8:00 Plenary Keynote Session (click here for more details)

9:00 Refreshment Break in the Exhibit Hall with Poster Viewing

IMMUNOTHERAPY VS. NGS-GUIDED TARGETED THERAPY FOR ONCOLOGY

10:05 Chairperson’s Remarks

Daniel H. Farkas, Ph.D., HCLD, Section Head, Molecular Pathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic

10:15 NGS-Based vs. Immunologic Therapies: Current Status, Future Directions

Davendra P. S. Sohal, M.D., M.P.H., Assistant Professor, Medicine; Staff, Hematology & Medical Oncology; Director, Clinical Genomics Program, Taussig Cancer Institute, Cleveland Clinic

Next-generation sequencing platforms have made precision oncology possible, and applications continue to grow. Meanwhile, immunotherapies are transforming cancer treatment. The two areas intersect more closely than it might appear, however. The role of tumor mutation burden, microsatellite status, and response-altering mutations make it imperative that we continue to apply NGS platforms to understand disease biology and response selection and prediction even better.

10:30 Perceptions versus Reality Surrounding Targeted Therapy and Immunotherapy

Terence Rhodes, M.D., Ph.D., Director, Immuno Oncology, Intermountain Healthcare

Oncologists and patients have never had more options for systemic cancer treatments. Patient perceptions of their cancer’s biology, their body’s immune system, and communication from media outlets may influence patient’s decisions among possible equivalent systemic therapy choices. Review of published and ongoing studies of targeted therapy and cancer immunotherapy can provide oncologists with information to help patients make informed, evidence-based decisions regarding their treatment.

10:45 Immunotherapy versus NGS-Guided Targeted Therapy: Promise and Pitfalls of Both Approaches

Jordi Rodon, M.D., Ph.D., Associate Professor, Investigational Cancer Therapeutics, Cancer Medicine, U. T. M. D. Anderson Cancer Center

Next generation sequencing, improved selectivity in targeted therapies and a vast amount of tumor biology knowledge generated by large initiatives such as The Cancer Genome Atlas (TCGA) has enabled Precision Medicine. Recent successes in Immuno-oncology have drifted investment and drug development portfolios towards novel immunotherapies. In the innovation cycle, hype produces inflated expectations that obscure science and clinical research. Drug development strategies require learning from the emerging clinical and translational data and from errors in the past as well as defining new paradigms of drug development that fit the purpose of each drug class.

11:00 PANEL DISCUSSION

NeoGenomics11:45 Next Generation Sequencing and Molecular Profiling in the Classification of Cancer
Maher Albitar, M.D.,  Senior Vice President, CMO, Director, Research and Development, NeoGenomics  
The role of NGS and molecular profiling in the classification of cancer will be discussed.  Various molecular approaches using NGS and how these approaches are currently used in cancer diagnosis, predicting prognosis and determining therapy will be discussed.  Clinical examples will be presented.  

12:00 pm  Sponsored Presentation (Opportunity Available)

12:15 Session Break

ConversantBio 12:25 Luncheon Panel Presentation I: Go Further. Faster: Cancer Diagnostics Need New Interdisciplinary Approaches to Improve Outcomes

Moderators:

Marshall Schreeder, CEO, Conversant Bio

Adel Mikhail, CEO, Folio

Panelists:

Dorothy French, DVM, Ph.D., DACVP, Director, Translational Pathology, Clinical Department, Abbvie Stemcentrix

Arnold B. Gelb, MD, MS, FASCP, FCAP, Clinical Advisor, Exploratory Biomarkers

Paul Van Hummelen, Ph.D., Senior Research Scientist, Division of Oncology, Department of Medicine Stanford University School of Medicine & Stanford Genome Technology Center

Beatrisa Boyadzhyan, Ph.D., Associate Director, Biomarker Discovery Group, Q2 Lab Solutions

Detecting cancer at actionable stages is the single best predictor of positive outcomes. Interdisciplinary efforts combining various technologies aim to detect cancer early and to personalize the diagnosis. Additional cross-disciplinary approaches are likely to improve survival.

12:55 Luncheon Presentation II (Sponsorship Opportunity Available)

1:25 Refreshment Break in the Exhibit Hall with Poster Viewing

PERSONALIZED MEDICINE TODAY AND TOMORROW: SCIENCE, BUSINESS, AND POLICY

2:00 Chairperson’s Remarks

Edward Abrahams, Ph.D., President, Personalized Medicine Coalition

2:10 Personalized Medicine – A Patient Perspective

Andrea E. Ferris, CEO, LUNGevity Foundation

2:25 A Pharmaceutical Industry Drug Developer’s Perspective on Personalized Medicine

Jean-Claude Marshall, MSc., PhD., Head of Clinical Genetics and Biospecimens, Early Clinical Development at Pfizer

Personalized medicine has evolved within the pharmaceutical industry. Rarely embraced 15 years ago, personalized medicine is now an integral component of drug discovery, development and commercialization. While it has improved many long-standing issues in the industry (high attrition for example), there are new challenges that come with this molecular diagnostic intensive approach, which in many circumstances changes the fundamental nosology of medicine as well as specific practice plans.

2:40In vitro Diagnostics - Changing Precision Medicine: The Expanding Role of Diagnostics in Driving Clinical Outcomes

Matt McManus, CEO, Asuragen

There is a demonstrated need in health care for the IVD industry to create tests that drive improved clinical outcomes. To achieve this, in partnership with Rx and Device companies, the industry's focus needs to be in 4 areas - 1) Test methods that accommodate content across the entire genome, 2) Deployability of testing, 3) Clinically relevant assay performance and 4) Ensuring reimbursement reflects value.

2:55 Personalized Medicine in an Academic Medical Center

Jason D. Merker, M.D., Ph.D., Assistant Professor, Pathology; Co-Director, Stanford Medicine Clinical Genomics Program, Stanford University School of Medicine

Exome and genome sequencing are being increasingly applied in clinical practice for the diagnosis of unexplained heritable disease. I will describe our experience establishing and running a clinical genomics program at an academic medical center.

3:10 Trends in Medicare Policy for Diagnostics in 2018

Bruce Quinn, M.D., Ph.D., Principal, Bruce Quinn Associates LLC

Medicare policy for precision medicine is rapidly evolving to meet new demands and resolve coverage issues for new technologies. A special local contractor policy program called MOLDX now handles coding, coverage, and payment for 80% of Medicare’s spending in genomics. PAMA law is being implemented in 2017/2018, and raising both new opportunities and new challenges for payment tactics. The most critical aspects of these issues will be discussed.

3:25 PANEL DISCUSSION

4:10 Valentine’s Day Celebration in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall

These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.

Next Generation Sequencing (NGS) in Precision Medicine

Prasun Mishra, Ph.D., Founder & CEO, Agility Pharmaceuticals

  • Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES)-based genome diagnostics
  • NGS-driven precision medicine approaches for hereditary cancers as an example
  • Utilizing cell-free DNA (cfDNA) for longitudinal patient monitoring
  • NGS applications in drug discovery and development

Isothermal Molecular Diagnostics as Alternatives to PCR

Robert Meagher, Ph.D., Research Scientist, Sandia National Laboratories

  • LAMP, NASBA, RPA, TMA, and more: sorting through the alphabet soup of techniques
  • Tradeoffs of sensitivity, specificity, and simplicity
  • Beyond resource-poor: designing assays and devices for use in awful conditions
  • Integrating assays with mobile technology
  • Intellectual property and licensing considerations

Lessons Learned: What I Wish I Had Known Before I Started Validation

Jason N. Rosenbaum, M.D., Assistant Professor, Pathology and Laboratory Medicine, University of Pennsylvania

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

Martin Siaw, Ph.D., MB(ASCP), Technical Consultant, Siaw Consulting

  • Selection of validation samples
  • Comparison to orthogonal assays
  • New CAP/AMP Guidelines
  • RNAseq in the clinical laboratory

    6:00 Close of Day

    Wednesday, February 14

    7:00 am Breakfast Presentation (Sponsorship Opportunity Available)  

    7:30 Registration Open and Morning Coffee

    8:00 Plenary Keynote Session (click here for more details)

    10:00 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall

    IMPLANTABLE AND WEARABLE BIOSENSORS

    10:50 Chairperson’s Remarks

    Michael P. Snyder, Ph.D., Chairman & Professor, Department of Genetics, Stanford University School of Medicine

    11:00 Wireless Sensors in Healthcare: Deceptive or Disruptive?

    Steven R. Steinhubl, M.D., Director, Digital Medicine, Scripps Translational Science Institute

    There is remarkable potential for wearable sensor technologies to enhance our understanding of individual variability in a wide range of physiologic responses in health and disease, but the path to incorporation into clinical care is fraught with challenges. In particular, there is currently a lack of high-quality evidence supporting the adoption of most of these technologies. Fortunately, there is a great deal of ongoing work to establish the true capabilities and potential value of this rapidly evolving field.

    11:30 Data Science for Physical Activity and Health

    Jure Leskovec, Ph.D., Associate Professor, Computer Science, Stanford University

    Understanding the basic principles that govern physical activity is needed to curb the global pandemic of physical inactivity. Our knowledge, however, remains limited owing to the lack of large-scale measurements of physical activity patterns across free-living populations worldwide. In this talk, we leverage the wide usage of smartphones with built-in accelerometry to measure physical activity at planetary scale. We find inequality in how activity is distributed within countries and that this inequality is a better predictor of obesity prevalence in the population than average activity volume. Reduced activity in females contributes to a large portion of the observed activity inequality. Our findings have implications for global public health policy and urban planning and highlight the role of activity inequality and the built environment for improving physical activity and health.

    12:00 pm Verily and the Project Baseline Study: A Platform for Discovery

    Jessica L. Mega, M.D., MPH, CMO, Verily Life Sciences (Formerly Google Life Sciences)

    This longitudinal cohort study will characterize participants across clinical, molecular, imaging, sensor, self-reported, behavioral, cognitive, environmental, and other health-related measurements including from onsite visits, continuous monitoring through sensor technology, and regular engagement via an online portal and mobile app. The study is the first initiative of Project Baseline, a broader effort designed to develop a well-defined reference, or “baseline,” of health as well as a rich data platform that may be used to better understand the transition from health to disease.

    12:30 Session Break

    12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

    1:10 Dessert Break in the Exhibit Hall and Last Chance for Poster Viewing

    MOLECULAR DIAGNOSTICS AT THE POINT-OF-CARE

    1:50 Chairperson’s Remarks

    Eric van Gieson, Ph.D., Program Manager, Program Manager, Defense Advanced Research Projects Agency (DARPA) Biological Technologies Office

    2:00 Genomic Sequencing in Clinical Care, When Will We Be There?

    Colleen S. Kraft, M.D., Associate Professor, Pathology & Laboratory Medicine, Emory University School of Medicine

    The advent of sequencing has revolutionized research and has influenced some clinical care. This talk looks at different platforms and where they are in actually being used for routine patient care in a healthcare setting, the goals, and limitations of this technology in the clinical setting.

    2:30 In-Q-Tel’s Investment Model as Applied to BioDetection, Analysis and Sample Prep Technology

    Kevin P. O’Connell, Ph.D., Vice President, Technology Staff, In-Q-Tel

    In-Q-Tel is the strategic investor for the US Intelligence Community. Our portfolio includes technologies that range from data analytics to hardware to biotechnology. This talk will provide a brief introduction to In-Q-Tel’s business model, with examples of investments in biotechnology from our portfolio.

    3:00 Metagenomic Nanopore Sequencing for Infectious Disease Diagnosis in Point-of-Care Settings*

    Charles Chiu, M.D., Ph.D., Associate Professor, Laboratory Medicine and Medicine, Division of Infectious Diseases; Director, UCSF-Abbott Viral Diagnostics and Discovery Center; Associate Director, Clinical Microbiology Laboratory, University of California, San Francisco

    Here we will discuss the applications and performance of diagnostic metagenomic sequencing on a pocket-sized nanopore sequencer (the MinIONTM by Oxford Nanopore Technologies) for pathogen detection, genomic surveillance, and characterization of antimicrobial resistance in point-of-care field settings. We will also describe the development of automated bioinformatics software on a high-end laptop for real-time sequencing analysis, taxonomic classification, and graphical visualization of results.

    *Arch Pathol Lab Med. 2017 Jun;141(6):776-786. doi: 10.5858/arpa.2016-0539-RA. Epub 2017 Feb 7. 

    Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Schlaberg R., Chiu C.Y., Miller S., Procop G.W., Weinstock G.; Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology; Microbiology Resource Committee of the College of American Pathologists.

    3:30 Session Break

    MOLECULAR DIAGNOSTICS AT THE POINT-OF-CARE (CONT.)

    3:40 Chairperson’s Remarks

    Eric van Gieson, Ph.D., Program Manager, Program Manager, Defense Advanced Research Projects Agency (DARPA) Biological Technologies Office

    3:45 Targeted NGS for Detection of Anti-Microbial Resistance: Microbes Are Not the Only Resistance that Must Be Overcome

    Crystal Jaing, Ph.D., Group Leader, Biosciences & Biotechnology Division, Applied Genomics, Lawrence Livermore National Laboratory

    A team of researchers has developed and pilot-tested a targeted amplification panel for over 500 Anti-Microbial Resistance (AMR) genes. Implemented using the AmpliSeq™ system for Ion platforms, we have found that ~5M targeted reads reliably finds AMR genes that are missed even when 100-200M unbiased reads are performed on the same complex samples. Challenges getting AMR panels accepted, plus attempts to support other NGS platforms will be discussed.

    4:15 Molecular Diagnostics in Austere Settings

    James V. Lawler, M.D., MPH, Director, International Programs and Innovation, Global Center for Health Security; Associate Professor, Medicine, Infectious Disease, University of Nebraska Medical Center

    Advancing technology continues to move diagnostics closer to the bedside, bringing us to the cusp of revolutionary changes in how physicians manage individual cases and how public health authorities address emerging disease threats. In this talk, we will explore implications for patient care and health security in developing and austere regions.

    4:45 PANEL DISCUSSION

    • What are the potential treatment impacts for point-of-care next-generation sequencing on antimicrobial resistant pathogens?
    • How will current, CLIA waived molecular diagnostics complement emerging point-of-care sequencing platforms?
    • Changes to clinical practice that will result with the ability to simultaneously identify thousands of diagnostic targets at the point-of-care
    • What approaches will lead to clinically relevant results, and highest likelihood of regulatory approval for point-of-care sequencing: Amplicon sequencing? Metagenomic analysis?

    5:15 Close of Conference Program


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