Advances in molecular diagnostics technologies have sparked innovation, expanded research capabilities, and enhanced clinical diagnostics. Cambridge Healthtech Institute’s Fourth Annual PCR and NGS-Based Diagnostics puts an emphasis on the technologies that drive personalized medicine, from PCR and NGS to microarrays, and showcases how they are being used to alter clinical outcomes. This event will provide a comprehensive look at integrating molecular diagnostics solutions for biomarker discovery and development, point-of-care, companion diagnostics, and infectious disease. Molecular technologies will be compared and evaluated and case studies on getting regulatory approval will be shared. Overall, this event provides insight into advanced techniques and tools for effective disease diagnosis.
Monday, February 20
10:30 am Conference Program Registration Open
11:50 Chairperson’s Opening Remarks
Tara Sigdel, Ph.D., Assistant Professor, Department of Surgery, University of California, San Francisco
12:00 pm Validation/QC Challenges for Germline Panels, Exomes, and Genomes
Josh Deignan, Ph.D., FACMG, Associate Director, UCLA Molecular Diagnostics Laboratories, Pathology and Laboratory Medicine, University of California, Los Angeles
The validation of next-generation sequencing tests is more complex than the validation of other molecular tests and often requires new approaches to address all of the required validation components. This talk will describe some of those new approaches.
12:30 Rapid Genome Sequencing in Neonatal Intensive Care
Rong Mao, M.D., FACMG, Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Assistant Professor, Pathology, University of Utah School of Medicine
Within the 4000 known single gene disorders, a significant fraction manifests symptoms during the newborn period. A rapid diagnosis of newborn diseases could make the difference between life and death and reduce length of stay in the neonatal intensive care unit (NICU). A targeted 4200 known disease-causing gene panel has been developed with a short turnaround and a focused interpretation combining genetics etiology with phenotype will provide a comprehensive clinical understanding of disease in NICU.
1:00 Session Break
1:10 Luncheon Presentation I: RNA in Liquid Biopsies – Promising New Biomarkers of Diseases
Peter Mouritzen, Vice President, Research & Development, Exiqon
To discover new biomarkers and develop minimal invasive tests, we have developed robust methods for NGS of smallRNA in biofluids. For high-throughput profiling microRNA in biofluids, highly sensitive LNA™-based qPCR is applied. Recent results will be discussed from the prostate cancer program.
1:40 Luncheon Presentation II (Sponsorship Opportunity Available)
2:10 Session Break
2:30 Chairperson’s Remarks
Tara Sigdel, Ph.D., Assistant Professor, Department of Surgery, University of California, San Francisco
2:40 Validation of Gene Biomarkers: Comparison of Two Gene Expression Assay Platforms Using FFPE Tissues
Tara Sigdel, Ph.D., Assistant Professor, Department of Surgery, University of California, San Francisco
Gene transcript (mRNA) biomarkers are useful as they can be quantified in laboratory setting using methods that are accessible to the researchers in both academic and commercial settings. Because of importance of the quality of generated data, it is in researchers’ interest to choose a better system in their research. Here we compared two gene expression quantification methods using probe based vs. conventional QPCR-based detection systems.
3:10 Recent Advances On Circulating MicroRNA Analysis
Kai Wang, Ph.D., Principal Scientist, Institute for Systems Biology
Circulating RNA, especially RNA encapsulated in lipid vesicles, has gained significant interest due to their possible clinical applications. Despite the potential, it is a challenge to accurately profile the circulating RNA. This is due to both sample and technical related issues. We made improvements on sequencing-based small RNA profiling as well as extracellular vesicle purification. These advances provide the foundation of moving this promising field forward.
3:40 Novel applications of dPCR
Rebecca Sanders, Ph.D., Researcher, Molecular Biology, Science and Innovation, LGC
With the development of ever growing numbers of molecular applications in fields such as diagnostics and synthetic biology, precision in validation and characterisation approaches is increasingly important. Digital (d)PCR has been shown to be accurate and precise, and can be used to interrogate new applications and complement their development. Here will be discussed the use of dPCR with expanding fields such as synthetic biology.
4:10 A Framework for the Quality Assessment of Measurement Procedures (QAMPS) Using in vitro Diagnostics
Michael Messenger, Ph.D., Head of Personalised Medicine and Health, University of Leeds; Deputy Director, NIHR Diagnostic Evidence Co-operative Leeds
In Vitro Diagnostic (IVD) medical devices form the basis of approximately 70% of clinical decision making in the NHS. The accuracy and associated uncertainty surrounding diagnostic testing consequently has a major impact on the overall quality of clinical decisions and subsequent clinical and cost effectiveness. We are not aware of any methods in use for evaluating the quality and appropriateness of measurement procedures within systematic reviews of IVDs. To address this issue, we have identified key parameters for consideration by systematic reviewers and developed a framework for Quality Assessment of Measurements Procedures, using IVDs. Herein we present a case study applying this framework, where several measurement parameters were identified that present a high risk of irreproducibility and inapplicability.
4:40 Refreshment Break and Transition to Plenary Session
5:00 Plenary Keynote Session
6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing
7:30 Close of Day
Tuesday, February 21
7:30 am Registration Open and Morning Coffee
8:00 Plenary Keynote Session
9:00 Refreshment Break in the Exhibit Hall with Poster Viewing
10:05 Chairperson’s Remarks
Karen A. Heichman, Ph.D., Vice President, Director, PharmaDx Program, ARUP Laboratories; Pathology, University of Utah
10:15 The FDA Review Process for Companion Diagnostic Devices
Soma Ghosh, Ph.D., Scientific Reviewer, FDA/CDRH/OIR/DMGP
Companion diagnostics have emerged as a powerful tool in personalized medicine allowing treatment decisions to be tailored for each patient. They are essential for the safe and effective use of many emerging and established therapeutic products, and promise a clearer understanding of disease development at the individual level. In the light of their expanding role in clinical decision making, my talk will focus on the critical regulatory review elements that FDA considers when evaluating companion diagnostic devices. I will illustrate key points using recent approvals as examples.
10:45 ARUP Laboratories’ Experience with FDA Approval of Companion Diagnostic (CDx) Tests within the Clinical Laboratory Environment
Karen A. Heichman, Ph.D., Vice President, Director, PharmaDx Program, ARUP Laboratories; Pathology, University of Utah
In December 2015, ARUP Laboratories received FDA approval for two CDx tests for Gleevec eligibility: KIT D816V Mutation Detection by PCR and PDGFRB FISH. These two tests are performed exclusively by ARUP as required under HDE regulations. ARUP established an augmented quality system integrated within the CLIA environment, which meets FDA requirements for medical devices, including a design control program. This presentation will address ARUP’s successful approach to CDx development.
11:15 Regulatory Pathways for NGS Applications and Other Advanced Technologies
Pamela Swatkowski, Director, Regulatory Affairs, Abbott Molecular
11:45 Panel with Session Speakers
12:15 pm Session Break
12:25 Luncheon Presentation I: Tackling the Challenge of FFPE DNA Extraction: An Automation Ready Solution Designed with an NGS Focus
JD Harper, Genomics Specialist, Automation & Genomics, Beckman Coulter Life Sciences
FormaPure DNA provides an automation-ready, SPRI-based extraction reagent kit to support your evolving research needs. Most notably, it provides significant time savings in reduced turnaround times and less than 15 minutes of hands-on time when automated on a Biomek.
12:55 Luncheon Presentation II (Opportunity Available)
1:25 Refreshment Break in the Exhibit Hall with Poster Viewing
2:00 Chairperson’s Remarks
Robert J. Meagher, Ph.D., Principal Member, Biotechnology and Bioengineering, Sandia National Laboratories
2:10 Targeted Sequence Capture (ViroCap) to Enhance the Sensitivity of Metagenomic Sequencing for the Detection of Viruses in Clinical Samples
Gregory Storch, M.D., Ruth L. Siteman Professor, Pediatrics, Washington University School of Medicine
Metagenomic sequencing is an emerging method for detecting microbial nucleic acids in clinical samples. We have developed a target-capture method (ViroCap) to enhance the sensitivity of metagenomic sequencing for detecting viruses in complex samples. Our results show dramatic increases in number of viruses detected, and breadth and depth of coverage. With this method, it is often possible to recover the complete viral genome directly from clinical samples.
2:40 FDA Experience with Emerging Genomics Technologies
Weida Tong, Ph.D., Director, Division of Bioinformatics and Biostatistics, NCTR/FDA
Emerging genomics methodologies contribute to our understanding of disease and health. However, its value in regulatory applications requires rigorous assessment and consensus between various stakeholders. The presentation overviews the FDA efforts in this field with a specific discussion of the FDA-led community-wide Microarray/Sequencing Quality Control (MAQC/SEQC). The new MAQC project, known as SEQC2, will be introduced which is focused on assessing the power and limitations of whole genome sequencing and target gene sequencing in clinical application.
3:10 Quenching of Unincorporated Amplification Signal Reporters (QUASR) for Robust Monitoring of Isothermal DNA and RNA Amplification Assays
Robert J. Meagher, Ph.D., Principal Member, Biotechnology and Bioengineering, Sandia National Laboratories
Isothermal nucleic acid amplification techniques such as LAMP are promising alternatives to PCR for point-of-need molecular diagnostics, but many of these techniques are hindered by relying upon non-specific detection chemistry. We present a simple, yet powerful modification to LAMP called QUASR that provides bright, multiplexable, target-specific signals with reduced false positives, high sensitivity even with complex sample matrices, and compatibility with simple instrumentation including a smart phone-based fluorescence imager.
3:40 Constructing an Atlas of the Human Metabolome to Enable Phenotyping and Genome Mapping
Mike Milburn, Ph.D., CSO, Metabolon
By producing a comprehensive read-out of an individual, we will describe how metabolomics is creating an “atlas” for understanding human health and disease and elucidating how major drivers like genetics, lifestyle and the microbiome exert their influence.
4:10 Hollywood Oscar Dessert Reception 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. Pre-registration to sign up for one of the topics will occur a week or two prior to the Event via the App.
Extracellular Vesicles and the Tumor Microenvironment
Muller Fabbri, M.D., Ph.D., Assistant Professor, Pediatrics and Molecular Microbiology & Immunology, Pediatric Hematology/Oncology, Children’s Hospital Los Angeles- University of Southern California
- How to best characterize the different populations of EVs (exosomes vs microvesicles vs large oncosomes)?
- How to isolate EVs from the plasma of patients?
- Can EVs be used as cancer diagnostic and prognostic biomarkers?
- How can EVs be used therapeutically?
Translating Great Laboratory Discoveries into Robust Field-Deployable Assays
Robert J. Meagher, Ph.D., Principal Member, Biotechnology and Bioengineering, Sandia National Laboratories
- Academic and Commercial perspectives on developing and deploying new technologies
- Translating from proof-of-concept to validation to FDA clearance
- How simple is simple enough? How complex is too complex?
- Intellectual property and licensing considerations
- Beyond resource-poor: designing assays and devices for use in awful conditions
Preparedness, Point-of-care Testing, and Global Resilience: Stopping Outbreaks and Assuring Equitable Care
Gerald J. Kost, M.D., Ph.D., M.S., FACB, Director, POC Testing Center for Teaching and Research (POCT•CTR), Pathology and Laboratory Medicine, School of Medicine, University of California Davis
- Assessing needs and country risks—Roundtable workshop example: Evaluation of Nigeria
- Diagnostic tests at the point of care and in isolation units (including floor plans)
- FDA Emergency Use Authorizations (EUAs) for Ebola virus disease, MERS-CoV, and Zika virus
- National POCT Policy and Guidelines—status, role, and future prospects
- Strategies for stopping outbreaks, epidemics, and pandemics
6:00 Close of Day
Wednesday, February 22
7:00 am Registration Open
7:00 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee
8:00 Plenary Keynote Session
10:00 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall
10:50 Chairperson’s Remarks
Weian Zhao, Ph.D., Assistant Professor, Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, University of California, Irvine
11:00 Emerging Technologies for Rapid Susceptibility Testing
Jennifer Dien Bard, Director, Clinical Microbiology Laboratory, Assistant Professor, Clinical Pathology, Keck School of Medicine of the University of Southern California
Despite significant advances in the approaches to pathogen identification directly from clinical specimens, antimicrobial susceptibility testing is mainly performed by conventional methods, delaying results by 2-5 days. There is an unmet need for rapid, phenotypic approaches to susceptibility testing directly from clinical specimens. The current multiplexed molecular panels available identify organisms directly from positive blood cultures and detect the presence of resistance markers. This session will summarize the current and emerging technologies for rapid phenotypic susceptibility testing.
11:30 Sizing Up Your Enemy: The Use of Molecular Tests to Predict Antimicrobial Resistance in Neisseria Gonorrhoeae
Peera Hemarajata, M.D., Ph.D., D(ABMM), Clinical Instructor, Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles
Neisseria gonorrhoeae has become a serious threat due to high prevalence of antimicrobial resistance. Prospective susceptibility testing enables physicians to use antimicrobials other than those recommended for empirical treatment, and could potentially delay emergence of resistance to recommended antibiotics. Few laboratories routinely perform culture and susceptibility testing for N. gonorrhoeae. We will discuss molecular assays that may be able to predict susceptibility directly from specimens without the need for culture.
12:00 pm Insights into Antimicrobial Resistance Learned from NGS
Susan Butler-Wu, Ph.D., D(ABMM), Associate Professor, Clinical Pathology, Keck School of Medicine of the University of Southern California, Director, Clinical Microbiology, LAC+USC Medical Center
12:30 Session Break
12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:10 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing
1:50 Chairperson’s Remarks
Paul Drain, M.D., MPH, FACP, Assistant Professor, Global Health, Medicine, and Epidemiology, University of Washington
2:00 Creating Molecular Point-of-Care Diagnostics for Use in Resource-Limited Settings: Lessons Learned from South Africa
Paul Drain, M.D., MPH, FACP, Assistant Professor, Global Health, Medicine, and Epidemiology, University of Washington
Although point-of-care diagnostics have been widely adopted worldwide, newer molecular tests are facing operational challenges in resource-limited settings. A rapid molecular diagnostic test for tuberculosis was introduced in South Africa, but studies have not demonstrated a significant clinical impact. This presentation will summarize studies on the application of the test in South Africa, as well as the critical lessons learned for the future design and implementation of advanced diagnostics for infectious diseases.
2:30 Point-of-Care Testing for Ebola and Other Highly Infectious Threats: Principles, Practice, and Strategies for Stopping Outbreaks
Gerald J. Kost, M.D., Ph.D., M.S., FACB, Director, POC Testing Center for Teaching and Research (POCT•CTR), Pathology and Laboratory Medicine, School of Medicine, University of California, Davis
We will identify key principles of point-of-care testing (POCT) for Ebola patients and others exposed to highly contagious diseases and assess evidence from recent crises, Ebola in West Africa, MERS in South Korea, and now, Zika. The goals are to stop the spread of disease and to prevent these types of epidemics from happening again. Hospitals that admitted Ebola patients mitigated risk by using POCT for critical care support in isolation units.
3:00 Nano for Mano: Developing Handheld Molecular Diagnostics with Nanotechnologies
Cesar M. Castro, M.D., Director, Cancer Program, MGH Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School
An inherent tension exists between clinical researchers’ molecular diagnostic needs and the practical realities of patient biopsies. Expanded and rapid protein profiling often requires ample specimen. Nanotechnologies create opportunities to extract adequate molecular readouts from less sample amounts. Coupled with advances in miniaturized devices, inroads have been made across disease types. This talk describes such multidisciplinary work in the oncology and infectious disease spaces as means to advance global medicine.
3:30 Session Break
3:40 Chairperson’s Remarks
Gerald J. Kost, M.D., Ph.D., M.S., FACB, Director, POC Testing Center for Teaching and Research (POCT•CTR), Pathology and Laboratory Medicine, School of Medicine, University of California, Davis
3:45 Deciphering the Code of Single EVs and RNPs Released from Glioblastoma Cells
Leonora Balaj, Ph.D. Research Fellow, Massachusetts General Hospital, Harvard Medical School
Tumor cells release a variety of content in the extracellular milieu that includes lipid-based vesicles as well as ribonucleoprotein (RNP) complexes. Lipid vesicles are termed extracellular vesicles (EV) and include vesicles ranging from 50nm to 1µm and above. mRNA, miRNA, ncRNA DNA and proteins have all been described to be present in the extracellular environment but it is currently unknown the extent to which each subpopulation is present at any given time. Data will be reported on counting of these molecules from two glioblastoma cells under normal and hypoxic conditions.
4:15 Exosomal MicroRNAs Regulate the Biology of the Tumor Microenvironment
Muller Fabbri, M.D., Ph.D., Assistant Professor, Pediatrics and Molecular Microbiology & Immunology, Pediatric Hematology/Oncology, Children’s Hospital Los Angeles - University of Southern California
MicroRNAs can be shuttled between different cell populations of the Tumor Microenvironment. The exchange of microRNAs affects the phenotype of cancer cells and surrounding cells contributing to cancer growth and resistance to therapy. Conversely, immune cells can affect cancer growth by releasing specific exosomic microRNAs. This lecture will focus on the role of exosomal microRNAs as central determinants of the biology of the tumor microenvironment and of cancer resistance.
4:45 Noncoding RNAs as Biomarkers in Gastrointestinal Cancer
Ajay Goel, Ph.D., Professor and Director, Center for Gastrointestinal Research, and Director, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center
Noncoding RNAs (ncRNAs) are emerging as important regulators of gene expression in cancer. Overexpression of specific noncoding RNAs (including microRNAs, SnoRNAs, piRNAs and circular RNAs) has been linked to the stepwise disease progression in colorectal cancer (CRC). Given their cancer-specific pattern of expression, remarkable stability and presence in blood and other body fluids, ncRNAs are considered to be highly promising cancer biomarkers. Accumulating evidence firmly supports the existence of unique ‘ncRNA signatures’ that can not only facilitate earlier detection of the tumor, but can also assist in predicting disease recurrence and therapeutic outcome to current treatment regimens.
5:15 Close of Conference Program