Cambridge Healthtech’s 6th Annual

Clinical Application of Circulating Biomarkers

From Discovery to a Clinically Robust Test

August 21-22, 2019

The detection of circulating biomarkers, including cell-free DNA (cfDNA) and circulating tumor cells (CTCs), is a game-changer for oncology and its application is spreading to other disease areas. The potential to diagnose cancer and other diseases early can truly revolutionize treatment and greatly alter care of patients, while reducing healthcare costs. Clinicians and technology developers alike are gathering and reviewing data to derive medical evidence that this technology is essential to the diagnosis and management of disease. Application of circulating biomarker assays in the clinical setting will be explored with the latest data presented. Join us this year to gain deep insights into the field and learn from leaders in the industry.

Final Agenda

Scientific Advisory Board

Luis A. Diaz, MD, Head, Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, Conference Chairman

Maximilian Diehn, MD, PhD, Assistant Professor, Radiation Oncology, Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University

Scott Kopetz, MD, PhD, FACP, Associate Professor, Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center

Abhijit Patel, MD, PhD, Associate Professor, Yale University School of Medicine

WEDNESDAY, AUGUST 21

10:30 am Registration

Constitution A&B
11:30 Plenary Keynote Session

11:30 Chairperson’s Remarks

Charles Mathews, Principal, ClearView Healthcare Partners

11:40 NEW: Plenary Keynote Presentation: FDA Updates: Now and Looking to the Future

Katherine Donigan, PhD, Acting Director of Personalized Medicine, Office of In Vitro Diagnostics and Radiological Health, Center for Devices and Radiological Health, U.S. Food and Drug Administration

Introduction and background of the new Office Director of OIR and updates on precision medicine and other initiatives at the FDA.

12:10-1:05 pm Plenary Keynote Discussion: Proposals and Solutions for Diagnostic Reform Including Oversight of Laboratory Developed Tests (LDTs)

Moderator:
Cynthia A. Bens, Senior Vice President, Public Policy, Personalized Medicine Coalition

• How are stakeholders influencing congressional activity on the Verifying Accurate Leading-edge IVCT Development (VALID) Act?
• How will the VALID Act change the current oversight landscape for diagnostics, including LDTs?
• How are policymakers addressing the role of CMS and CLIA in the VALID Act?
• How will increased regulatory and oversight activities at the FDA affect the diagnostics industry?
• What impact will changes in diagnostics regulation and oversight have on patient care?

Panelists:

Julie Khani, MPA, President, American Clinical Laboratory Association (ACLA)

Donald E. Horton, Jr., Senior Vice President, Global Government Relations & Public Policy, Laboratory Corporation of America Holdings

Susan Van Meter, Executive Director, AdvaMedDx

Tara Burke, PhD, Senior Director, Public Policy & Advocacy, Association for Molecular Pathology (AMP)

Laura Lasiter, PhD, Science Policy Analyst, Friends of Cancer Research

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

1:35 Ice Cream & Cookie Break in the Exhibit Hall with Poster Viewing

CLINICAL APPLICATIONS OF METHYLATED DNA
Constitution A

2:05 Chairperson’s Opening Remarks

Scott Kopetz, MD, PhD, FACP, Associate Professor, Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center

2:10 Genomic Location of DNA Methylation Biomarker Development

James G. Herman, MD, Hematology/Oncology, Professor of Medicine, UPMC Endowed Chair for Lung Cancer Research; Co-Director, Lung Cancer Program, University of Pittsburgh

DNA methylation alterations in cancer are promising targets for the development of diagnostic, prognostic, and predictive biomarkers. Ultrasensitive methods for detection can improve early cancer detection. However, effective development of DNA methylation-based biomarkers is often limited by suboptimal assay design, which includes consideration of genomic location. We will examine the importance of genomic location in DNA methylation biomarker development for uses in cancer, and discuss particular issues related to circulating tumor DNA.

2:40 Applications of Mutation-Agnostic Detection of Circulating Tumor DNA Using Methylation Profiling

Filip Janku, MD, PhD, Associate Professor, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center

Detection of circulating tumor DNA can be used for molecular diagnostics, assessment of efficacy of cancer therapy and detection of minimal residual disease. Most currently used approaches utilize detection of well-defined molecular alterations such as hot spot mutations, which can limit applicability especially in patients without clinically detectable disease. Unlike detection of hot spot mutations, methylation profiling can identify tumor DNA irrespective of underlying mutation profile. Integrating methylation profiling into detection of circulating tumor DNA can increase sensitivity and help to transition molecular testing of circulating tumor DNA from metastatic cancers to early stages.

3:10 A DREAM Come True – Assessing Heterogeneous Methylation with Digital Microfluidics for Enhanced Detection of Rare Tumor DNA

Thomas R. Pisanic II, PhD, Research Scientist, Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University

Aberrant DNA methylation is commonly heralded as a promising cancer biomarker; however, its inherently stochastic nature often leads to variable methylation patterns that can complicate the use of methylation biomarkers for clinical diagnostics. Here we demonstrate how incorporation of our novel assay strategy termed DREAMing into a digital microfluidic platform allows for facile assessment of intermolecular methylation heterogeneity and enhances diagnostic performance in challenging samples such as liquid biopsies.

3:40 Drop-off Assay Using Crystal™ Digital PCR for the Detection and Quantification of EGFR Mutations in Circulating cfDNA 

Romain Parillaud, PhD, Application Specialist, Stilla Technologies

Using Crystal™ Digital PCR, a 3-color multiplex drop-off assay was developed to detect NRAS, KRAS, and EGFR mutations in circulating cell-free DNA samples of non-small cell lung cancer patients. Furthermore, a unique 6-color target multiplexing drop-off assay was validated to monitor the most prevalent EGFR mutations in the patient samples.

4:10 Refreshment Break in the Exhibit Hall with Poster Viewing

DISEASE MONITORING
Constitution A

4:55 Chairperson’s Remarks

Scott Kopetz, MD, PhD, FACP, Associate Professor, Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center

5:00 CSF Tumor DNA for the Detection and Monitoring of Central Nervous System Cancers

Chetan Bettegowda, MD, PhD, Jennison and Novak’s Families Chair, Departments of Neurosurgery and Oncology, Johns Hopkins University School of Medicine

There are no existing biomarkers for the diagnosis and monitoring of nearly all central nervous system tumors. Circulating biomarkers for CNS tumors are present in diminished levels compared to those in the cerebrospinal fluid. CSF-tDNA has been shown to be elevated in a myriad of CNS neoplasms. This talk will discuss the application of CSF-tDNA for the detection and monitoring of tumors involving the central nervous system.

5:30 Development of a Translational Pipeline for EV-Based Liquid Biopsies

Jennifer C. Jones, MD, PhD, Investigator, Laboratory of Pathology; Head, Translational Nanobiology Section, Center for Cancer Research, NCI, NIH

Tumor cells, immune cells, and irradiated tissues release large quantities of biologically active (and distinct) nanoscale extracellular vesicles (e.g., exosomes and microparticles). Dr. Jones is developing improved methods to characterize, sort, and perform functional studies of nanoparticles, and has established a translational EV analysis pipeline, with instrumentation for preparation, analysis, counting, and cytometric study of extracellular vesicles.

6:00 Beyond Histology: Using Circulating Tumor DNA to Augment Clinical Trial Patient Selection

Yelena Y. Janjigian, MD, Chief, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center

My talk will cover application of cfDNA technology in clinic, specifically innovation in clinical trial design and patient selection. We will review trials in progress and cover challenges in interpretation of cfDNA results, contribution of clonal hematopoiesis and tumor heterogeneity to discordant results.

6:30 Close of Day

6:30 Dinner Short Course Registration*

*Separate registration required.

THURSDAY, AUGUST 22

7:15 am Registration

Independence B-E and Foyer
7:30 Problem Solving Breakout Discussions with Continental Breakfast

Current Status of ctDNA in Disease Monitoring

Moderator: Christine Parseghian, MD, Assistant Professor, Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center

• Current status of ctDNA in disease monitoring
• Potential of ctDNA monitoring in clinical management of advanced cancers
• Potential of ctDNA monitoring in clinical trials for advanced cancers

KEYNOTE SESSION

8:25 Chairperson’s Remarks

Abhijit Patel, MD, PhD, Associate Professor, Yale University School of Medicine

8:30 Perspectives of Liquid Biopsies in Genomics-Driven Oncology

Michael R. Speicher, MD, Professor and Chairman, Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz

Genome-driven oncology may have enormous potential to change the clinical management of patients with cancer. To this end, liquid biopsies, i.e. components of tumors, which are shed into the circulation, such as circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs), are increasingly being used for monitoring tumor genomes and to identify predictive biomarkers. Current and future perspectives of liquid biopsies and their impact on genomics-driven oncology will be presented.

9:15 Development of NGS ctDNA Assays for Oncology Translational and Clinical Research

Brian Dougherty, PhD, MBA, Executive Director, Translational Science, Oncology IMED, AstraZeneca

AstraZeneca has been investigating the use of ctDNA testing for patient selection, drug resistance emergence, and patient monitoring. Additional studies have extended studies into exosomal DNA and transcriptome sequencing. I will also present a recently published orthogonal bench-marking study of commercial ctDNA assays that determined most tumor-plasma discordance is due to assay technical performance, not tumor heterogeneity or clonal hematopoiesis.

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

CLINICAL TRIAL PROGRESS AND GUIDING TREATMENT DECISIONS
Constitution A

11:00 Chairperson’s Remarks

Abhijit Patel, MD, PhD, Associate Professor, Yale University School of Medicine

11:05 Value of ctDNA in Monitoring and Guiding Therapy in Advanced Cancer

Christine Parseghian, MD, Assistant Professor, Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center

Advances in ctDNA analyses allow reliable detection and quantification of tumor mutations in real-time. Dynamic changes in ctDNA levels provides a highly specific noninvasive tool for early assessment (up to 16 weeks prior to radiographic change) of treatment response. This allows early selection of patients likely to respond and helps avoid toxicities. We propose ctDNA as a tool to refine monitoring and management of metastatic cancers in clinics and clinical trials.

11:35 Blood-Based Assays for Monitoring of Treatment Response in Glioma Patients

Leonora Balaj, PhD, Instructor of Neurosurgery, Massachusetts General Hospital

We performed longitudinal whole-transcriptome profiling of serum exosomes from patients suffering from recurrent glioblastoma (GBM) enrolled in a clinical trial to assess response to Dacomitinib, a second-generation irreversible EGFR tyrosine kinase inhibitor. All patients had failed standard of care therapy and had tumors amplified for EGFR. They underwent daily oral administration of Dacomitinib and blood serum samples were collected immediately prior to first treatment and monthly thereafter. Deep sequencing of exosomal RNA (exRNA), derived from just 2 ml of patient serum, revealed robust signatures of treatment response, as defined by >6-month progression-free survival. Non-responders were found to have significantly elevated levels of a number of transcripts including colony stimulating factor 1 (CSF1), which regulates the proliferation, differentiation, and survival of macrophages and microglia. We further identified robust signatures of treatment response in post-treatment serum samples, including the suppression of DNA methyltransferase 3 alpha (DNMT3a), an important player in DNA methyl transfer for de-novo methylation, as well as Adenosine A2B receptor (ADORA2B), a member of the G protein-coupled receptor superfamily which is overexpressed in a variety of cancers and has been shown to play a role in tumor progression via increased angiogenesis and metastasis. Furthermore, we identified general decreases in oncogene abundance following Dacomitinib treatment, including tumor protein p53 (TP53) and Ovo like transcriptional repressor 1 (OVOL1), a zinc finger containing transcription factor, shown to be a critical inducer of epithelial-tomesenchymal transition in cancer. Finally, in comparison to healthy control serum we find hundreds of transcripts exhibiting differential abundance in pre-treatment GBM patients that may serve as general non-invasive biomarkers for this devastating disease. This study is unique because it represents the first longitudinal profiling of the exosomal transcriptome in a cohort of genomically selected GBM patients. These findings are a tantalizing step toward exosome-based biomarkers for the detection of GBM, as well as patient stratification and monitoring.

12:05 pm Redefining Adjuvant Therapy in the Era of Circulating Biomarkers

Jamie E. Chaft, MD, Medical Oncologist, Memorial Sloan Kettering Cancer Center

Solid tumors have long been defined by TNM staging, providing risk of disease recurrence and death. Stage and other clinical features are used to prescribe adjuvant therapy. This system over treats many and misses some who may benefit. Logical trial designs using circulating biomarkers will lead to smaller trials with greater impact per intervention studied, moving towards an era of precision cancer care in the curative setting.

12:35 Enjoy Lunch on Your Own

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

EARLY DETECTION
Constitution A

2:15 Chairperson’s Remarks

Luis A. Diaz, MD, Head, Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, Conference Chairman

2:20 Therapy Monitoring and Early Detection via ctDNA: Progress and Challenges

Abhijit Patel, MD, PhD, Associate Professor, Yale University School of Medicine

Our group has developed NGS-based methods that use molecular and computational error suppression techniques to enable ultrasensitive detection of ctDNA based on genomic and epigenomic features. This presentation will describe our work in the areas of therapeutic response assessment and early cancer detection.

2:50 Sensitive Tumour Detection and Classification Using Plasma Cell-Free DNA Methylomes

Scott V. Bratman, MD, PhD, Radiation Oncologist, Radiation Medicine Program; Scientist, Princess Margaret Cancer Centre, University Health Network; Assistant Professor, Depts of Radiation Oncology and Medical Biophysics, University of Toronto

Sequencing of somatic mutations in plasma cell-free DNA (cfDNA) may have low sensitivity among early-stage cancer patients given the limited availability of recurrent mutations. In contrast, DNA methylation patterns, which are tissue and cancer-type specific, are not similarly constrained. Here, we demonstrate the performance of genome-wide methylome analysis of plasma cfDNA for cancer detection and classification across an extensive collection of plasma samples from multiple tumor types.

3:20 Somatic Mutations and HPV as a Biomarker for Head and Neck Squamous Cell Carcinoma

Nishant Agrawal, MD, Professor of Surgery, Director of Head and Neck Surgery Oncology, University of Chicago

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide. HNSCC develops in the oral cavity, pharynx, and larynx and is associated with tobacco exposure, alcohol abuse, and infection with oncogenic viruses. Despite global advances in cancer care, HNSCC often presents with advanced disease and is associated with poor 5-year survival of ~50%. Conventional analysis of tissue through cytopathology or histopathology are the mainstay of diagnosis. Furthermore, there are no useful biomarkers for disease diagnosis or surveillance. With recent advances, tumor and HPV DNA for HNSCC diagnosis, monitoring, and surveillance, is emerging as a biomarker in HNSCC. In HNSCC, analysis of tumor DNA has the potential to enhance tumor profiling, aid in determining patient prognosis, and guide treatment decisions.

3:50 Why Is It So Hard to Develop Molecular Markers for Cancer Screening? Lessons from CRC Screening

David F. Ransohoff, MD, Professor, Medicine and Epidemiology, University of North Carolina, Chapel Hill

Developing molecular markers – like a blood test – for cancer screening has been a ‘holy grail’ in cancer research since the 1970s, when initial results for carcinoembryonic antigen (CEA) showed nearly 100% sensitivity and specificity for colon cancer, only to be followed by disappointing results in later research. Lessons from past failures and from to-date modest successes can illustrate the challenges in this field and how to address them.

4:20 End of Summit