Cambridge Healthtech Institute’s Inaugural
Sample Prep, Assay Development and Validation
Pre-Analytical Considerations for Biomarkers and Diagnostics
August 22-23, 2018 | Grand Hyatt Washington | Washington, DC
Developing a highly sensitive, reproducible and robust molecular assay may be a challenge regardless of whether it is an IVD or an LDT assay. Novel sample preparation technologies significantly increase sensitivity and specificity of a test that is run on a heterogeneous sample or a sample that contains a low concentration of analyte. Rapid sample-to-result technologies help cut down turnaround time while decreasing the cost of a test. Cambridge Healthtech Institute’s Inaugural Sample Prep, Assay Development and Validation conference is designed to bring together leading industry and academia experts in biospecimen science and molecular diagnostics to discuss major challenges and latest advances in sample preparation for advanced molecular diagnostics technologies as well as development and validation of NGS and other advanced diagnostics assays.
Final Agenda
Recommended Short Course*
SC7: Practical Considerations for NGS Data Analysis and Interpretation
Robert D. Daber, PhD, Founder and CEO, Gnosity Consults
Matthew Lebo, PhD, FACMG, Director, Bioinformatics, Partners Personalized Medicine; Instructor, Pathology, Brigham and Women’s and Harvard Medical School
*Separate registration required
WEDNESDAY, AUGUST 22
7:45 am Registration and Morning Coffee (Independence Foyer)
8:25 Chairperson’s Opening Remarks
Julie Ramage, National Account Director, Diagnostics, Pfizer Oncology
8:30 KEYNOTE PRESENTATION: Prerequisite to Precision Medicine
Carolyn Compton, MD, PhD, Professor of Life Sciences, School of Life Sciences, Arizona State University; Professor of Laboratory Medicine and Pathology, Department of Pathology, Mayo Clinic School of Medicine
The future of precision medicine depends on molecular diagnostics to guide decision-making at every level of medical intervention. Of primary importance in diagnostics development is the quality of the starting materials – the biospecimens - used for analysis. The bar for biospecimen quality is high. The diagnostics development community must address the need for standardized preanalytical processes for biospecimens to accelerate the development of accurate, reproducible, clinically relevant molecular diagnostics for precision medicine.
9:00 Tissue Handling and the Impact on DX/CDX in Precision Medicine
Julie Ramage, National Account Director, Diagnostics, Pfizer Oncology
With the evolving complexity of testing methodologies in somatic disease, the need for quality and quantity of tissue becomes an important facet of the patient’s pathway to treatment and options. The need to address the actual sample handling at the time of extraction should be the primary goal of each stakeholder, including the companies developing the diagnostic testing and the pharma companies involved in therapies for treatment.
9:30 Pre-Analytical and Analytical Considerations for Cell-Free DNA Profiling
Dana W. Y. Tsui, PhD, Assistant Attending, Pathology, Memorial Sloan Kettering Cancer Center
Our expanding knowledge of cancer genomes has led to the development of more effective therapeutic strategies. Tumor profiling has shown clinical benefits to improve precision medicine, and the possibility of performing noninvasive molecular profiling using liquid biopsy is highly promising. The talk will give examples to illustrate the potential of cell-free DNA analysis to address the limitation of tumor profiling to improve patient stratification and treatment management, and also discuss the pre-analytical and analytical considerations, from sample collection to data reporting, for clinical deployment.
10:00 Combined and Fully Automated DNA Isolation & NGS Library Preparation
Richard Montagna, PhD, FACB, Senior Vice President, Scientific & Clinical Affairs, Rheonix, Inc.
The Encompass Optimum™ Workstation automatically isolates DNA and prepares NGS libraries using a variety of different commercial kits. Compared to manually prepared libraries, the automatically prepared libraries exhibit excellent quality metrics. The ability to combine DNA isolation and library preparation on a single instrument dramatically reduces cost and time.
10:30 Coffee Break in the Exhibit Hall with Poster Viewing (Independence Ballroom)
11:10 Chairperson’s Remarks
Raja Luthra, PhD, Professor, Hematopathology, The University of Texas MD Anderson Cancer Center
11:15 Circulating Cell Free Tumor DNA (ctDNA) Genotyping in Cancer Patient Management
Raja Luthra, PhD, Professor, Hematopathology, The University of Texas MD Anderson Cancer Center
Ultrasensitive genotyping technologies have created a niche for cell free tumor DNA (ctDNA) mutation testing in cancer patient management. However, ctDNA genotyping can be challenging due to low amounts of ctDNA, lack of standardization of pre-analytic and analytical variables and background noise affecting the reliability of detecting low-level mutations. The presentation will discuss challenges with ctDNA testing and highlight critical steps involved in implementation of ctDNA genotyping for individualized patient management.
11:45 Complementary Detection Of Somatic Variants From Tumor Tissue And Plasma Samples Using AVENIO Analysis Kits
Alex Lovejoy, PhD, Principal Scientist I, Roche Sequencing
Tissue based testing, often using archived formalin-fixed, paraffin embedded samples is considered to be the gold standard for tumor molecular profiling. However, when tumor tissue is unavailable, non-invasive liquid biopsy, which enables the analysis of circulating tumor DNA may be used as an alternative sample type. We have developed robust, complementary next-generation sequencing based assays to sensitively detect somatic mutations from tumor tissue and plasma samples by overcoming unique sample type specific challenges.
12:05 Considerations with Liquid Biopsy in vitro Diagnostic Tests
Karen Bijwaard, MS, RAC, MB(ASCP), Scientific Master Reviewer, Molecular Pathology and Cytology Branch, Division of Molecular Genetics and Pathology, Office of In Vitro Diagnostics and Radiological Health, U.S. Food and Drug Administration
Assays utilizing cell-free/circulating-tumor DNA are rapidly being employed in the clinical oncology setting to aid in patient management. The utilization of these assays brings unique regulatory challenges regarding their use in patient management and as companion diagnostics. The complexities associated with the clinical and analytical validation of cf/ctDNA based in vitro diagnostic devices (IVDs), highlighting points to consider when validating the performance of the assays.
12:25 pm Direct Circulating Tumor DNA Detection in Metastatic Colon Cancer from Unpurified Plasma Using a Digital PCR Platform
Nasrin Sarafan-Vasseur, PhD, Research Engineer, Genetics, Rouen University Hospital, Inserm
In standard pre-analytical conditions, an isolation step is required for circulating tumor DNA (ctDNA) analysis from plasma samples. We have performed a pilot study that aimed to evaluate the ctDNA detection by digital PCR platform directly in plasma. Using 43 blood samples from patients with metastatic colorectal cancer (mCRC), we compared the detection rate and mutant allelic frequencies (MAF) between the plasma group (PG) without and after isolation step (IG). Our results showed that direct detection of ctDNA from plasma is a feasible approach, particularly from samples with high Mutant allele frequency (MAF) > 0.5%.
12:45 Enjoy Lunch on Your Own
1:15 Session Break
1:45 Chairperson’s Remarks
Carolyn Hiller, Program Director, Clinical Diagnostics, Medical Device Innovation Consortium
1:50 Development of Computer Assisted Diagnostics Based Testing in the Clinical Laboratory
Orly Ardon, MSc, MBA, PhD, R&D Program Manager, ARUP Laboratories/University of Utah
Computer assisted diagnostics refers to the use of artificial intelligence for the processing and analysis of digital images. Our laboratory is involved with several initiatives to improve clinical operations by developing and integrating computer assisted diagnostics that can replace several manual microscopy-based tests. The proposed presentation will cover historical developments in the use of microscopy for scientific research as well as for diagnostic patient care and describe how computer assisted diagnostics is now being integrated in our clinical lab operations.
2:20 Implementation of Prostate Biopsy Tissue Print Technologies for Molecular Biomarker Discovery and Testing
Sandra Gaston, PhD, Director, Molecular Biomarkers Research Laboratory, Pathology and Laboratory Medicine, Tufts Medical Center
With the introduction of multiple tissue-based tests for cancer, the allocation of formalin fixed paraffin embedded biopsy tissues has become challenging. We have developed and fully implemented tissue print technologies that allow us to obtain high quality RNA and DNA from prostate biopsy cores without compromising the tissue for pathology diagnosis. Importantly, we have demonstrated that tissue print technologies provide a practical and cost-effective approach to biopsy-based biomarker testing that is feasible in both hospital and office practice settings.
2:50 Harmonized Education: Using Surrogate Samples in IVD Development and Regulatory Submission
Carolyn Hiller, Program Director, Clinical Diagnostics, Medical Device Innovation Consortium
Surrogate samples, when properly used decrease time needed for analytical testing and reduce costs for test development and submission. A framework collaboratively developed by industry and FDA establishes a foundation for surrogate use to support innovation and product submissions. Educational materials to use the framework were developed to speed patient access to innovative technology.
3:20 Refreshment Break in the Exhibit Hall with Poster Viewing (Independence Ballroom)
4:00 Computational Approaches to Extract Multiple Sources of Genome Variation from Suboptimal Tumour Specimens
Trevor Pugh, PhD, FACMG, Scientist, Princess Margaret Cancer Centre, University Health Network, Assistant Professor, Department of Medical Biophysics, University of Toronto
We are developing laboratory and computational approaches to extract multiple sources of genome variation from suboptimal tumour specimens, and to integrate these data types into cohesive portraits of individual tumour biology. Part of our work focuses on translation of these findings into clinical practice through nomination of clinically-informative markers for targeted testing and development of bioinformatics tools to support clinical laboratory workflows.
4:30 Comprehensive DNA and RNA Profiling in Solid Tumors for the Detection of Targetable Kinase Fusions
Ryma Benayed, PhD, Technical Director, Clinical Next Generation Sequencing Laboratory, Assistant Attending, Pathology, Memorial Sloan Kettering Cancer Center
Kinase gene fusions have emerged as major therapeutic targets in different tumor types. They are routinely detected by hybridization capture-based DNAseq assays via tiling of the genomic regions involved; however, this may not effectively detect all fusion events especially when resulting from complex rearrangements. We have evaluated the importance of targeted RNAseq for the identification of fusions that are driver negative by MSK-IMPACTTM, a custom, FDA-authorized 468-gene clinical sequencing panel.
5:00 Droplet-Based Microfluidic Detection of Pathogens
Charles Young, PhD, Principal Professional Staff, Assistant Program Manager, Applied Biology Group, Asymmetric Operations Sector, The Johns Hopkins University Applied Physics Laboratory
Even with the advent of rapid molecular and immunological detection methods in environmental and clinical laboratories, there are many instances where growth and isolation of the organism is necessary to confirm results of rapid methods, determine whether the organisms are living or dead, or for follow-on analysis. In this presentation, we will describe our current efforts to apply a rapid, droplet-based microfluidic method for the growth-based differential detection and isolation of microbes in as little as 4 hours.
5:30 Networking Reception in the Exhibit Hall with Poster Viewing (Independence Ballroom)
6:30 Close of Day
THURSDAY, AUGUST 23
7:15 am Registration (Independence Foyer)
7:30 Problem Solving Breakout Sessions with Continental Breakfast (Independence F-I)
This session features various discussion groups that are led by a moderator/s who ensures focused conversations around the key issues listed. Attendees choose to join a specific group and the small, informal setting facilitates sharing of ideas and active networking. Continental breakfast is available for all participants.
AI for Image Analysis
Moderator: Orly Ardon, MSc MBA PhD, R&D Program Manager, ARUP Laboratories/University of Utah
- Major developments in artificial intelligence and digital imaging in healthcare
- Incorporation of machine learning tools into classic diagnostics lab practices
- Partnerships between labs and machine learning start ups
Tissue Printing for Biomarker Studies and Beyond
Moderator: Sandra Gaston, PhD, Director, Molecular Biomarkers Research Laboratory, Pathology and Laboratory Medicine, Tufts Medical Center
- Key considerations when designing biomarker studies that utilize human tissue biospecimens
- Emerging new applications of tissue print technologies
- Using tissue prints to analyze molecular biomarkers in biopsies and other limited high-value tissue specimens
8:25 Chairperson’s Remarks
Benjamin Wunsch, PhD, Materials Science & Engineering, Surface Chemist, Staff, Nanobiotechnology, IBM Research, IBM
8:30 Extracellular Vesicles for Precision Medicine
Jennifer C. Jones, MD, PhD, Molecular Immunogenetics & Vaccine Research Section, Vaccine Branch, CCR, NCI
Tumor cells, immune cells, and irradiated tissues release large quantities of biologically active (and distinct) nanoscale extracellular vesicles (e.g., exosomes and microparticles). Our laboratory is developing improved methods to characterize, sort, and perform functional studies of nanoparticles, and has established a flow cytometry pipeline, with instrumentation for preparation, analysis, counting, and cytometric study of extracellular vesicles.
9:00 Exosome Extraction Using Silicon Nanostructures
Benjamin Wunsch, PhD, Materials Science & Engineering, Surface Chemist, Staff, Nanobiotechnology, IBM Research, IBM
Well-defined nanostructures for separation of biological colloids present a next step in the engineering of separation medium, providing enhanced precision and resolution with tunability of design. Using Nanoscale Deterministic Lateral Displacement (nanoDLD) devices fabricated using silicon nanolithography, we demonstrate the ability to separate and enrich extracellular vesicles such as exosomes from biological fluids. On-chip separation with nanoDLD provides a tunable, precision, continuous flow module for fully integrated liquid biopsy development.
9:30A High-Throughput FFPE-NGS Solution That Improves Workflow Efficiency And Results For Cancer Biomarker Discovery
Han Wei, PhD, Senior Applications Scientist, Beckman Coulter Life Science
10:00 Coffee Break in the Exhibit Hall with Poster Viewing (Independence Ballroom)
11:15 am Chairperson’s Remarks
11:20 am - 12:00 pm TECHNOLOGY PANEL: Disruptive Technologies in Lab Medicine
Moderator: Gregory J. Tsongalis, PhD, HCLD, CC, Professor, Pathology; Director, Laboratory for Clinical Genomics and Advanced Technology (CGAT), Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center and The Audrey and Theodor Geisel School of Medicine at Dartmouth
- What is appropriate test utilization?
- How do you ensure both user and patient safety?
- How are tests implemented in the clinical setting?
- How do they get regulated?
- How do results get reported?
- How do you enforce quality control in implementation?
- How does it impact emerging applications such as liquid biopsies, infectious disease outbreaks, and POC diagnostics?
Panelists:
Rakesh Nagarajan, MD, PhD, Chief Biomedical Informatics Officer, PierianDx
Greg Richard, Chief Commercial Officer, Interpace Diagnostics
Crystal R. Icenhour, PhD, CEO, Aperiomics, Inc.
Additional Panelists to be Announced
12:00 - 12:45 pm Changing Approaches to Sustainable Funding in Diagnostics
Moderator: Bruce Quinn, MD, PhD, Principal, Bruce Quinn Associates
Today, many innovators in the diagnostics industry struggle for funding, and yet news of large scale acquisitions or large (over $30M) funding rounds pops up regularly. How can innovators better understand the changing dynamics of the funding environment to succeed? How can investors know if they are getting exposed to the potentially best investments? Whether government or private, what drives the final difficult decisions and how can companies raise their chances of success? This session features leaders from several different channels of funding for innovators, including the NIH, other federal programs, and corporate and traditional venture investors.
Panelists:
Alex DeWinter, PhD, Managing Director, GE Ventures
Tyler Merkeley, BARDA’s CARB-X Program Manager, Health Scientist, Division of CBRN Countermeasures, BARDA
Todd Haim, PhD, Program Director, National Cancer Institute SBIR Development Center
David Sans, PhD, MBA, F.A.A.R.M., Managing Director, Healthcare Capital Markets, THINK EQUITY (A Division of Fordham Financial Mgmt., Inc.)
Wouter Meuleman, PhD, Director, Venture Investments, Illumina Ventures
12:45 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:15 Close of Sample Prep, Assay Development and Validation
Recommended Dinner Short Course*
Recommended Short Course*
SC9: Microfluidics and Lab-on-a-Chip Devices for POCT: Technologies and Commercialization
Chris Myatt, Founder & CEO, MBio Diagnostics, Inc
Marta Fernandez Suarez, Daktari Diagnostics & FIND
Additional Instructors to be Announced
*Separate registration required