PCR and NGS-Based Molecular Diagnostics

Advances in molecular diagnostics technologies have sparked innovation, expanded research capabilities, and enhanced clinical diagnostics. Cambridge Healthtech Institute’s Fifth 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 12

10:30 am Conference Program Registration Open

NEXT-GENERATION SEQUENCING IN PRECISION MEDICINE

11:50 Chairperson’s Opening Remarks

Apostolia-Maria Tsimberidou, M.D., Ph.D., Professor, Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center

12:00 pm Optimization of Precision Medicine in the Era of Immunotherapy

Apostolia-Maria Tsimberidou, M.D., Ph.D., Professor, Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center

The availability of novel immunotherapeutic agents and targeted therapy holds the promise of expediting the availability of precision medicine in the treatment of cancer. Development of clinically meaningful biomarkers and optimization of clinical trials will improve the clinical outcomes of patients with advanced cancer. Objectives: 1) optimization of use of targeted therapy, 2) immunotherapy as targeted therapy: biomarker development, 3) completed and ongoing clinical trials to expedite the implementation of precision medicine.

12:30 Different Whole Genome Sequencing Strategies for the Clinical Management of Patients with Oropharyngeal Squamous Cell Carcinoma

David I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology, Chairman of the Technology Assessment Group, Center for Individualized Medicine, Mayo Clinic

1:00 Session Break

Codexis NEW1:10 Luncheon Presentation I: An Engineered DNA Ligase for Efficient Conversion of Input DNA during NGS Library Preparation

John Nicols President & CEO Codexis, Inc.

Molecular diagnostics NGS assays are critically dependent on efficient conversion of low-concentration DNA samples to sequencing-capable fragments via adapter ligation. An engineered DNA ligase was developed to achieve exceptional conversion of low-concentration input DNA, with improved reaction kinetics relative to T4 ligase, while maintaining low adapter dimerization activity. The Codexis Performance DNA Ligase is ideally suited for NGS IVD applications, where it will improve assay sensitivity and increase workflow flexibility and robustness.

1:40  Session Break

CLINICAL NGS ASSAYS AND VALIDATION

2:30 Chairperson’s Remarks

Apostolia-Maria Tsimberidou, M.D., Ph.D., Professor, Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center

2:40 Panel Discussion
Moderator: Apostolia-Maria Tsimberidou, M.D., Ph.D., Professor, Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center

3:10 Clinical and Informatic Approaches to Genomic Screening of Ostensibly Healthy Individuals

Matthew Lebo, Ph.D., Director, Bioinformatics; Assistant Professor, Pathology, Brigham and Woman’s Hospital, Harvard Medical School

This talk will focus on approaches to implement a genomic screening program for unselected cohorts. Specific considerations will be placed on the clinical informatics components required to scale variant annotation, filtration, review, and reporting. Results from several studies will highlight key considerations and outcomes when utilizing different approaches.

3:40 Challenges of Validating NGS Assays: Using Hearing Loss Gene Panel as an Example

Rong Mao, M.D., FACMG, Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Assistant Professor, Pathology, University of Utah School of Medicine

With the advent of massively parallel sequencing methodologies, the number of genes implicated in human disease has increased substantially in the last decade. This has led to a surge in the number of clinical laboratory tests offered to detect genetic causes of inherited disorders. As more clinical laboratories tread the unfamiliar ground of NGS, they are faced with the challenges of establishing validation and quality control processes. Here I am using a hearing loss gene panel as an example to discuss validating the NGS assay, limitations of the assay, and CAP/FDA guidelines.

4:10Validation of RNA Fusions for an NGS Based Clinical Assay

Helen Fernandes, Ph.D., Co-Director, Genomic Oncology, Columbia University
This presentation will focus on the design, development, and validation of an NGS assay to detect RNA fusions from FFPE tissue. The advantages of using highly multiplexed reference materials to achieve faster development time, lower validation costs, improved performance, and for submission to state regulatory agencies will be discussed.

4:25 Nuclease-Activated Probe (NucAP) Technology for Cancer Detection 
Shambhavi Shubham, Ph.D., Postdoctoral fellow, Department of Internal Medicine, University of Iowa 

4:40 Refreshment Break and Transition to Plenary Session

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

 

Precision for Medicine6:00 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

TECHNOLOGIES FOR BACTERIAL PROFILING AND ANTIBIOTIC SUSCEPTIBILITY TESTING

10:05 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

10:15 One-Step, Rapid Detection of Antibiotic Resistant Bacteria in Blood Stream Infections Using High Volume Droplet Blood PCR

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

Antibiotic resistance represents a major global health threat. Lack of rapid diagnostics in the current paradigm of clinical microbiology, especially for bloodstream infections (BSIs), has resulted in use of inappropriate or unnecessarily broad-spectrum antibiotics, which are associated with significantly increased morbidity, mortality and healthcare cost as well as having the potential to select for resistant strains. In this presentation, we will discuss a new high throughput blood droplet PCR technology for rapid bacterial detection directly in blood samples without culture and sample processing.

10:45 Rapid Phenotypic Antibiotic Susceptibility Testing Directly from Clinical Samples Using Single-Molecule Counting

Rustem Ismagilov, Ph.D., Professor, Chemistry & Chemical Engineering, California Institute of Technology

Rapid antibiotic susceptibility testing (AST) is critical for delivering care and enabling antibiotic stewardship. Phenotypic AST is the gold standard, but is unacceptably slow, requiring pre-culture steps. Genotypic AST has not been sufficiently general to replace the gold standard (especially in Gram-negative organisms). We use SlipChip for digital single-molecule counting of pathogen-specific RNA and DNA to perform phenotypic AST directly from clinical samples in as fast as 30 minutes.

11:15 Developing Ultrasensitive Molecular Methods for Rapid Bacterial Identification and Antibiotic Resistance Profiling

Shana Kelley, Ph. D., Professor, Department of Pharmaceutical Sciences, University of Toronto

We are developing several different platforms for rapid bacterial analysis and the detection of antibiotic resistance. Devices that enable genetic analysis in heterogeneous samples will be described. 

11:45 Enjoy Lunch on Your Own

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

PERFORMANCE CRITERIA AND DRUG DISCOVERY APPLICATIONS

2:00 Chairperson’s Remarks

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

2:10 Regulatory Innovation: Keeping Pace with NGS atop the Shifting Sands of Precision Medicine

Peggy Carter, Ph.D., Global Head, Regulatory Affairs, Oncology Precision Medicine, Novartis

Regulatory innovation may no longer be an oxymoron. The “one drug, one test” paradigm in precision medicine is not sustainable and we look to technologies such as NGS and new ways of regulatory thinking to move to the next level. Recent examples of first-of-their kind approvals in the precision medicine space reveal the beginnings of a much-needed paradigm shift.

2:40 Setting Up a Framework to Facilitate Implementation of Performance and Design Standards for Clinical NGS

Birgit Funke, Ph.D., FACMG, Vice President, Clinical Affairs, Veritas Genetics; Associate Professor, Pathology, Harvard Medical School

Next-generation sequencing (NGS)-based testing has transitioned from a niche technology to widespread adoption in clinical testing. Numerous recommendations and guidelines provide high level education but detailed and practical implementation support is lacking. This presentation describes an effort led by the College of American Pathologists (CAP) that provides systematic step-by-step education to guide clinical testing laboratories through all steps of the lifecycle of a clinical NGS test.

3:10 Towards Design Control for LDTs: Establishing Performance Criteria for NIPT

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

CLIA requires that high complexity laboratories establish and verify performance characteristics before introducing a new testing procedure. Laboratory developed procedures (LDPs) may be validated under CLIA and CAP accreditation standards, while ISO15189 accreditation and FDA clearance specifies that validation/verification must be performed under design control. This presentation will discuss establishing, validating and verifying performance characteristics under design control for LDPs, using non-invasive prenatal testing (NIPT) as an example.

3:40 Using Genetics to Select Safer Targets and Drugs

Lucas D. Ward, Ph.D., Senior Scientist, Human Genetics and Functional Genomics, Comparative Biology and Safety Sciences, Amgen

Genetics is increasingly being used in two major ways: to discover new targets through variation in populations (studying diseases), and to stratify drug response clinically (studying patients; pharmacogenetics). Early-stage genetic validation often focuses more on efficacy than safety. I will discuss how genetics can be used, even pre-clinically, to improve safety: anticipating target-mediated adverse events, which we have demonstrated are statistically linked to target genetics; and constructing drug selectivity panels.

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, and 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, PhD, 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, PhD, 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

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

PCR & NGS TECHNIQUES AND TECHNOLOGIES

10:50 Chairperson’s Remarks

Gregory Storch, M.D., Ruth L. Siteman Professor, Pediatrics, Washington University School of Medicine

11:00 Relative Roles of PCR and NGS for Viral Diagnosis

Gregory Storch, M.D., Ruth L. Siteman Professor, Pediatrics, Washington University School of Medicine

Several important trends are occurring in diagnostic virology. Amplification-based testing is maturing, with increasing availability of FDA-approved and cleared assays. Some testing is moving towards centralized platforms in core laboratories while other testing is moving centrifugally to near and at point-of-care locations. NGS offers very exciting potential for nonbiased detection. This talk will describe these trends and their interrelationships.

11:30 MPseq and Its Applications to the Clinical Setting

George Vasmatzis, Ph.D., Co-Director, Biomarker Discovery Program, Center for Individualized Medicine; Consultant, Department of Molecular Medicine; Associate Professor, Molecular Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN

We have developed MPseq, an accurate and inexpensive whole genome sequencing platform that has been used to detect structural variants. MPseq is a combination of a protocol and algorithms that can replace several cytogenetic tests and provide comprehensive diagnostic value with high specificity, sensitivity and cost-effectiveness. Most importantly our process can provide a detailed description of all DNA rearrangements at a resolution that can show how individual genes are disturbed thus providing necessary novel insight for correct clinical interpretation.

12:00 pm Molecular Detection of Emerging Pathogens in Low-Resource Settings

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

Emerging infectious diseases often occur in parts of the world that lack even the most basic infrastructure that underlies modern clinical diagnostics. We summarize developments in molecular assays, sample prep, and detection that increasingly allow laboratory-quality diagnostic assays to be performed in low-resource settings, including our own work with smartphone-based detection of viral pathogens. We also discuss limitations of these techniques and open areas of inquiry, including tradeoffs between simplicity and assay performance.

12:30 Session Break

12:40 Enjoy Lunch on Your Own

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

PCR & NGS TECHNIQUES AND TECHNOLOGIES (CONT.)

1:50 Chairperson’s Remarks

Gregory Storch, M.D., Ruth L. Siteman Professor, Pediatrics, Washington University School of Medicine

2:00 GV9 – A New, Sensitive and Economic Method for Species-Level 16S Bacterial Characterization

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

16S methods currently employed are, generally, limited to analysis of a single hypervariable region which makes taxonomic classification difficult beyond the genus level without a substantial false positive rate. To address this issue, a novel method, named GV9, has been developed to enhance species level calls and abundance estimates through simultaneous analysis and dynamic selection of multiple hypervariable regions.

2:30 Multiplex Real-Time PCR Assays that Assess the Abundance of Rare Mutations Associated with Cancer

Fred Kramer, Ph.D., Professor, Microbiology, Biochemistry & Molecular Genetics, Public Health Research Institute, Rutgers University

“SuperSelective” PCR primers, due to their unique design, amplify rare mutant DNA fragments in liquid biopsy samples, while ignoring abundant related wild-type fragments. Multiplex PCR assays utilize SuperSelective primers that contain unique 5’-tag sequences, enabling each different amplicon to be detected with a differently colored molecular beacon probe. As many as 35 different mutations can be assessed simultaneously. These assays are extraordinarily sensitive, rapid, and inexpensive.

3:30 Session Break

COMPARISON OF METHODS

3:40 Chairperson’s Remarks

Kai Wang, Ph.D., Principal Scientist, Institute for Systems Biology

3:45 The Prospect of PCR & NGS-Based Molecular Diagnostics

Kai Wang, Ph.D., Principal Scientist, Institute for Systems Biology

Circulating nucleic acids, especially cell-free DNA, has been the center of most NGS-based molecular diagnostics in recent years. Even though the circulating RNA isn’t as well developed as DNA in clinical application yet, it has tremendous potential. Several factors may impact the analysis of circulating nucleic acids. We will address and discuss some of the possible issues.

4:15 A Non-Invasive Urinary Common Rejection Module (uCRM) QPCR Gene Expression Score for Kidney Transplant Injury

Tara Sigdel, Ph.D., Assistant Professor, Surgery, University of California, San Francisco

Urine offers an attractive source of biomarkers for urological and kidney related diseases. A qPCR assay for a gene panel as a biomarker for kidney transplant rejection and injury has been developed and optimized. The talk will summarize the strategy for discovery and validation of this assay which is highly relevant in other diseases as well.

4:45 Comparison of Gene Expression Profiles on nanoString vs. Fluidigm qPCR Platforms on Human Renal Allograft Biopsies

Dejan Dobi, M.D., Postdoctoral Scholar, Pathology, University of California, San Francisco

We conducted a performance comparison study between nanoString’s nCounter platform (barcoded oligonucleotide-based technology for gene-expression analysis) and standard (Fluidigm) qPCR on matched FFPE and RNA later-preserved human kidney allograft biopsies. In addition to demonstrating the feasibility of the nanoString platform on FFPE samples, we show various applications to address biologically relevant questions in the renal transplant setting.

5:15 Close of Conference Program

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