Cambridge Healthtech Institute’s Inaugural

NGS Advances and Multimodality Assays

NGS Technology Trends and New Applications

August 26-27, 2020


Next-generation sequencing (NGS) has become an integral part of molecular diagnostics, with applications ranging from inherited disorders and oncology, to infectious disease, to prenatal diagnostics. NGS-based assays are getting more sophisticated as they are combined in cohesive assays with other detection technologies and modalities. CHI's Inaugural NGS Advances and Multimodality Assays conference will focus on the latest NGS developments, including whole genome sequencing as a diagnostics platform, as well as on multiomics and multimodality assays.

WEDNESDAY, AUGUST 26

10:30 am Registration

Plenary Keynote Session

11:30 AM Chairperson’s Remarks

11:35 Diagnostic Technologies that Will Shape Precision Medicine in 2020 and Beyond

David Walt, PhD, Hansjörg Wyss Professor, Biologically Inspired Engineering, Harvard Medical School; Professor, Department of Pathology, Brigham and Women’s Hospital; Core Faculty, Wyss Institute for Bioinspired Engineering, Harvard University, HHMI Professor

Precision medicine is being driven by the ability to measure biomarkers at an unprecedented scale. New technologies that enable the measurement of proteomic and genomic signatures, engineered nanomaterials for diagnostics and imaging, smart watches, and new imaging modalities provide personalized profiling that can be used to guide therapies. In order for these technologies to have the greatest benefit, there will need to be profound changes in the entire diagnostics ecosystem.

12:05 PM PANEL DISCUSSION: What Technologies Will Shape Precision Medicine in 2020?

Moderator: Susan Hsiao, MD, PhD, Assistant Professor, Pathology and Cell Biology, Columbia University Medical Center

Panelists: Jonathan Nowak, MD, PhD, Assistant Professor, Pathology, Harvard Medical School; Associate Pathologist, Brigham and Women’s Hospital

David Walt, PhD, Hansjörg Wyss Professor, Biologically Inspired Engineering, Harvard Medical School; Professor, Department of Pathology, Brigham and Women’s Hospital; Core Faculty, Wyss Institute for Bioinspired Engineering, Harvard University, HHMI Professor

What is the clinical impact of some of the following technologies and what are the current bottlenecks and challenges that need to be surmounted? Examples of each will be given:

  • RNA sequencing
  • Single-cell sequencing and analysis
  • AI and machine learning
  • Tumor mutational burden measurement
  • Emerging uses of NGS
  • Tumor microenvironment
  • Multi-modality and transcriptomics
  • Microbiome

12: 35 Plenary Keynote Introduction

Charles Mathews, Principal, ClearView Healthcare Partners

12:45-1:15 Fireside Chat

Moderator: Charles Mathews, Principal, ClearView Healthcare Partners

Sara Brenner, MD, MPH, Associate Director for Medical Affairs; CMO, In Vitro Diagnostics, Office of In Vitro Diagnostics & Radiological Health (OIR), Office of Product Evaluation & Quality (OPEQ), Center for Devices & Radiological Health (CDRH), U.S. Food & Drug Administration

1:15 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:45 Refreshment Break in the Exhibit Hall with Poster Viewing

BREAKTHROUGHS AND NOVEL APPLICATIONS

2:15 Chairperson’s Opening Remarks

2:20 The Intersection of Knowledge Informatics and Clinical NGS Platforms

Carl Morrison, MD, DVM, Senior Vice President, Pathology, Roswell Park Comprehensive Cancer Center

New technologies in NGS are emerging that allow for more efficient clinical laboratory workflows. Matching knowledge informatics to the output of these new NGS technologies is essential to moving the field of clinical sequencing forward.

2:50 Cell-by-Cell: Building High-Resolution Tumor Atlases

Asaf Rotem, PhD, Associate Director, Center for Cancer Genomics, Dana-Farber Cancer Institute

After years of improved cancer therapy, we still struggle to understand malignancies. A major obstacle is our lack of understanding of cancer complexity and its microenvironment. In the last years, we and others developed tools to uncover the transcriptomes of patient-derived single cells. This cutting-edge approach, complimented with other technologies, is central in understanding tumors by creating detailed atlases.

3:30 Harmonization and Concordance of NGS-Based Assays for Patient Selection in NCI Precision Medicine Trials

Nina Lukinova, PhD, Program Director, National Cancer Instite

Examples from MATCH and PedMATCH clinical trials that enroll patients based on perfectly harmonized targeted NGS assays performed in five different labs, as well as current enrollment for rare tumors, is ongoing based on the results from 30 sequencing laboratories with different panels.

3:50 Sponsored Presentation (Opportunity Available)

4:20 Refreshment Break in the Exhibit Hall with Poster Viewing

MULTIPLEX PANELS

5:05 Chairperson’s Remarks

Esther Babady, PhD, Medical Director, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center

5:10 Head-to-Head Comparison: Nanopore Sequencing and Microarray Resequencing for Multiplex Pathogen Identification

Robert Duncan, PhD, Principal Investigator, Office of Blood Research and Review, Center for Biologics Evaluation and Research (CBER), FDA

GeneChip Resequencing microarrays have been advanced for infectious disease agent detection and identification from Ebola to Zika. Next-generation sequencing with the highly mobile and costeffective nanopore sequencing device is challenging the supremacy of the microarray in rapid point-of-need pathogen detection. This talk will present results of side-by-side application of these two platforms for detection in pathogen-spiked blood samples and compare their performance.

5:30 Syndromic Testing for Meningitis/Encephalitis: Saga of the Love-Hate Relationship

Jennifer Dien Bard, PhD, D(ABMM), Director, Microbiology and Virology, Children’s Hospital Los Angeles; Associate Professor, Pathology and Laboratory Medicine, Keck School of Medicine, University of Southern California

As part of the Multiplex Panel session, this talk will focus on multiplex testing for the laboratory diagnosis of meningitis and encephalitis as compared to standard-of-care testing. The potential benefits and limitations of panel testing for meningitis and encephalitis compared to standard-of-care testing will be discussed. The potential approaches to maximize testing yield will also be discussed.

5:50 The Biofire Pneumonia Panel: Does It Relate to Microbiological and Clinical Variables?

Kenneth Rand, MD, Medical Director, Clinical Microbiology Laboratory; Professor, Pathology and Medicine, University of Florida

The BioFire FilmArray Pneumonia Panel (PP) detects 15 common bacterial pathogens semi-quantitatively (copy # from 104 to 107), 3 atypical pneumonia bacteria, 8 viruses, and 7 antimicrobial resistance markers by multiplex PCR in about 1 hour in the laboratory. Results of our 396-patient study suggest PP detects more bacterial isolates than conventional microbiology, and the copy number correlates with outcome variables, such as ICU length of stay, temperature, and white cells in the BAL. Results reported in a 3–4 h timeframe after a BAL could potentially improve both antibiotic choice and de-escalation in critically ill intubated patients.

6:10 PANEL DISCUSSION: Advancing Multiplex Panels for Clinical Diagnostics

Moderator: Esther Babady, PhD, Medical Director, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center

Panelists: Robert Duncan, PhD, Principal Investigator, Office of Blood Research and Review, Center for Biologics Evaluation and Research (CBER), FDA

Jennifer Dien Bard, PhD, D(ABMM), Director, Microbiology and Virology, Children’s Hospital Los Angeles; Associate Professor, Pathology and Laboratory Medicine, Keck School of Medicine, University of Southern California

Kenneth Rand, MD, Medical Director, Clinical Microbiology Laboratory; Professor, Pathology and Medicine, University of Florida

Tim Blauwkamp, PhD, CSO, Karius

  • Comparison of multiplex platforms
  • Reimbursement considerations
  • Proving clinical utility of multiplex diagnostic tests

6:40 Close of Day

6:40 Dinner Short Course Registration*

7:00 - 9:30 Dinner Short Course*

Recommended Dinner Short Course*

SC6: Microfluidics and Lab-on-a-Chip Devices for POCT: Technologies and Commercialization

*Separate registration required.

THURSDAY, AUGUST 27

7:15 am Registration

7:30 Problem Solving Breakout Discussions with Continental Breakfast

OPPORTUNITIES AND CHALLENGES OF EARLY DIAGNOSIS OF DISEASE

8:25 Chairperson’s Remarks

John Sninsky, PhD, Independent Consultant, Translational Medicine and Science

8:30 KEYNOTE PRESENTATION: Overdiagnosis and Premature Treatment Challenge of Early Disease Detection

Laura Esserman, MD, MBA, Professor, Surgery, University of California San Francisco Medical Center

9:00 Multi-Modal Approaches to Early Disease Detection and Population-Based Screening

Drew Watson, MBA, PhD, Biostatistics and Clinical Development Advisor

For many diseases, population screening is essential to improving patient survival. Despite the promise of blood-based “liquid biopsies”, progress has been limited, necessitating new multi-omics approaches that incorporate multiple technologies. We discuss new approaches to biomarker discovery, algorithm development, and clinical validation using mechanistic, statistical, and machine learning approaches for handling multi-omics data. We further discuss the need to improve clinical decision support systems to facilitate clinical decision making.

9:30 Epigenetic Genomic Modifiers as Proxies of Gene Expression for Cancer

Alex Aravanis, MD, PhD, CSO, Head, R&D, Co-Founder, GRAIL

10:00 Coffee Break in the Exhibit Hall with Poster Viewing

NUCLEIC ACID DETECTION

11:00 Chairperson’s Remarks

11:05 Global Considerations with Nucleic Acid at POC

Nardev Ramanathan, PhD, Global Lead Analyst, Digital Transformation, Lux Research, Inc.

Point-of-care (POC) capabilities for nucleic acid testing offer huge opportunities here to tackle this unmet need. Many recent advances are bringing us closer to this reality, mostly around microfluidics and miniaturization of biosensors. However, there are still other considerations to be had around population and sociodemographic differences that will impact how these technologies will be implemented and deployed. This talk will tackle the global considerations for nucleic acid POC using case studies of currently deployed medical technologies as examples.

11:35 Engineering Biology for Diagnostic Solutions

William Blake, PhD, CTO, Sherlock Bioscience

SHERLOCK is a method for single molecule detection of nucleic acid targets and stands for Specific High Sensitivity Enzymatic Reporter unLOCKing. It works by amplifying genetic sequences and programming a CRISPR molecule to detect the presence of a specific genetic signature in a sample, which can also be quantified. When it finds those signatures, the CRISPR enzyme is activated and releases a robust signal. This signal can be adapted to work on a simple paper strip test, in laboratory equipment, or to provide an electrochemical readout that can be read with a mobile phone.

12:05 pm Instrument-Free Paper-Based POC Pathogen Diagnostics for the Clinic and the Home

Paul Yager, PhD, Professor, Department of Bioengineering, University of Washington

Instruments ranging from the venerable GeneXpert to ones just coming on the market allow fairly rapid NAAT pathogen detection, but they are based on disposable cartridges and a permanent (and relatively expensive) instrument. Our lab has been developing instrument-free disposable NAAT devices that retain the advantages of the instrumented systems, but free the user from the need for purchasing a permanent instrument (and the upfront cost that incurs).

12:35 Sponsored Presentation (Opportunity Available)

1:05 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:35 Refreshment Break in the Exhibit Hall with Poster Viewing

CLINICAL METAGENOMIC SEQUENCING

2:15 Chairperson’s Remarks

Norman Moore, PhD, Director, Scientific Affairs, Abbott

2:20 Clinical Metagenomic Sequencing and Human Host Response: Changing the Diagnostic Paradigm?

Charles Chiu, MD, PhD, Professor, Laboratory Medicine and Medicine/Infectious Diseases, Director, UCSF-Abbott Viral Diagnostics and Discovery Center; Associate Director, UCSF Clinical Microbiology Laboratory, UCSF School of Medicine

Metagenomic next-generation sequencing (mNGS) is a transformative technology for infectious disease diagnosis as it enables detection of nearly all pathogens – viruses, bacteria, fungi, and parasites – in a single assay. Here we will discuss the integration of multiple approaches to enhance the clinical utility of body fluid mNGS, including nanopore sequencing, CRISPR-Cas12-based pathogen detection, complementary host response analyses, and simultaneous diagnosis of cancer.

2:50 Mycobacterial Infections in Immunocompromised Patients: The Perfect Fit for Metagenomic Solutions

Nathan Ledeboer, PhD, Professor and Vice Chair, Pathology; Medical Director, Medical College of Wisconsin

DETECTION OF RESISTANCE

3:20 Applying Next-Generation Sequencing for Detection of Antimicrobial Resistance

Patricia Simner, PhD, D(ABMM), Associate Professor, Pathology; Director, Bacteriology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine

3:50 Flash: A Next-Generation CRISPR Diagnostic for Multiplexed Detection of Antimicrobial Resistance Sequences

Emily Crawford, PhD, Scientist II, Infectious Disease Initiative, Chan Zuckerberg Biohub

4:20 End of Summit



Premier Sponsor


Corporate Sponsors


View All Sponsors