Cambridge Healthtech Institute’s Third Annual

Circulating Cell-Free DNA

Clinical Directions and Emerging Avenues for Early Detection

March 10-11, 2016 | Hilton San Francisco Union Square | San Francisco, CA
Part of the 23rd International Molecular Medicine Tri-Conference


Circulating cell-free DNA (cfDNA) currently allows for minimal residual disease detection and treatment monitoring with new clinical data emerging regularly. However, as technology evolves and assays increase in sensitivity, the possibility of earlier detection will become more of a reality. At Cambridge Healthtech Institute’s Third Annual Circulating Cell-Free DNA, leading researchers from academia and industry will come together to address advances as well as existing challenges in this rapidly growing field. This year’s event will place emphasis on early detection, clinical validation of assay sensitivity and specificity, and establishing standards for cfDNA.

Final Agenda

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Thursday, March 10

7:30 am Registration and Morning Coffee


8:25 Chairperson’s Opening Remarks

Chris Karlovich, Ph.D., Principal Scientist, Molecular Diagnostics, Clovis Oncology

» 8:30 KEYNOTE PRESENTATION: Deep Sequencing of Circulating Tumor DNA for Personalized Cancer Detection and Monitoring

Maximilian Diehn, M.D., Ph.D., Assistant Professor, Radiation Oncology, Stanford University

I will describe the development and application of CAPP-Seq, a deep sequencingbased method for ultra-sensitive and specific detection of circulating tumor DNA that is broadly applicable to different cancer types and clinical scenarios.

9:10 Clinical Applications of an NGS Assay for Ultrasensitive Measurement of ctDNA

Abhijit Patel, M.D., Ph.D., Assistant Professor, Yale University School of Medicine

Our group has developed an ultrasensitive, multi-target NGS-based assay that can identify and quantify mutant ctDNA using novel error-suppression techniques. Broad coverage of mutation hotspots and warm-spots allows detection of ctDNA without prior knowledge of the tumor’s mutation profile. Data will be presented from various ongoing studies to establish the clinical utility of this technology.

9:40 Assay Characterization for Clinical Applications

Rebecca Leary, Ph.D., Lab Head & Research Investigator, Genomics Group, Next Generation Diagnostics, Novartis

Evaluation and characterization of cell-free DNA technologies is a critical step when introducing these assays for the analysis of clinical specimens.

10:10 Multiplexed ICE COLD PCR Enriches Any Low-Level Mutation Present in DNA Isolated from FFPE and Plasma Samples

Katherine Richardson, Ph.D., Vice President, Research & Development ,Transgenomic, Inc

Using Multiplexed ICE COLD-PCR, cancer patients’ DNA isolated from FFPE & Plasma was utilized to enrich for any low level mutations present in the samples. The results demonstrated detection of low level mutations in liquid biopsies; thus allowing for disease management with respect to treatment options and/or drug cocktail modifications for cancer patients.

10:40 Coffee Break with Exhibit and Poster Viewing


11:15 Pretreatment Assessment and Serial Monitoring of EGFR Mutations from NSCLC Patients Treated with Rociletinib (CO-1686)

Chris Karlovich, Ph.D., Principal Scientist, Molecular Diagnostics, Clovis Oncology

We are exploring blood-based molecular testing in clinical trials of rociletinib (CO-1686), a novel third-generation TKI that selectively inhibits the EGFR activating and T790M resistance mutations in NSCLC patients. The utility of plasma-based EGFR mutational analysis for diagnosis, as a PD biomarker, and for ongoing monitoring of response to rociletinib will be described.

11:45 Monitoring Cancer through the Blood

Cloud P. Paweletz, Ph.D., Head, Translational Research Laboratory; Biomarker Lead, Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute

Genomic alterations in genes such as EGFR, ALK, KRAS, and BRAF have been validated as powerful predictive biomarkers in the management of non-small cell lung cancer (NSCLC), colorectal cancer, and melanoma; testing for these mutations is currently standard to personalize treatment decisions. The challenges associated with routine use of NGS include availability of adequate tumor specimens, slow turnaround time, and evolving tumor biology in response to treatment that may necessitate a repeat biopsy to guide subsequent therapy. Here we discuss the use of blood based, non-invasive test to diagnose, monitor and understand lung cancer.

12:15 pm Pharmacodynamic Assessment of Drug Response by Monitoring Mutational Load in Urinary Circulating Tumor DNA

Mark G. Erlander, Ph.D., CSO, Trovagene

The concept of liquid biopsies is expanding to include urine as a specimen type. Using DNA extraction process that isolates systemic ctDNA and a quantitative PCR-NGS enrichment method for mutation detection at a single copy level, we demonstrate that drug-induced immediate early changes in ctDNA mutational load correlate with tumor burden and treatment response. As a non-invasive specimen, urine enables development of novel algorithms to inform treatment decisions via frequent monitoring of ctDNA.

12:45 Luncheon Presentation to be Announced

1:15 Session Break


1:50 Chairperson’s Remarks

Nishant Agrawal, M.D., Associate Professor, Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine

2:00 Application of Tumor-Derived DNA in the Management of Individuals
with Cancer

Chetan Bettegowda, M.D., Ph.D., Assistant Professor, Neurological Surgery, Johns Hopkins University School of Medicine

The development of non-invasive methods to detect and monitor tumors continues to be a major challenge in oncology. The molecules of tumor derived DNA can be distinguished from the background of normal DNA by the presence of somatic mutations. Using sensitive digital PCR based approaches, we have been able to query bio-fluids from a number of human malignancies for levels of tumor derived DNA (ct-DNA). We will present our efforts at detecting ctDNA in a number of different solid tumors and the potential clinical applications of this approach.

2:30 Glypican-1 Identifies Cancer Exosomes and Detects Early Pancreatic Cancer

Raghu Kalluri, M.D., Ph.D., Professor, Department of Cancer Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer

Using mass spectrometry analyses, we identify a cell surface proteoglycan, glypican-1 (GPC1), specifically enriched on cancer-cell-derived exosomes. GPC11 circulating exosomes (crExos) were monitored and isolated using flow cytometry from the serum of patients and mice with cancer. GPC11 crExos may serve as a potential non-invasive diagnostic and screening tool to detect early stages of pancreatic cancer to facilitate possible curative surgical therapy.

3:00 Refreshment Break with Exhibit and Poster Viewing

3:30 Maximizing Next-Generation Sequencing Capabilities
of Circulating, Cell-Free DNA

Timothy Harkins, President & CEO, Swift Biosciences

Swift Biosciences presents NGS methods that are cost effective, sensitive, and specific to assess cfDNA. Methods discussed for whole genome sequencing from PCR-free libraries, point mutation detection with hyb/capture and multiplex amplicons, and methylation patterns all from single liquid biopsy samples.

4:00 PANEL DISCUSSION: Clinical Implementation of cfDNA

Moderator: Dan Grosu, Sequenom

Panelists: Sabita Sankar, Ph.D., Director, Business Development, Biodesix

Abhijit Patel, M.D., Ph.D., Assistant Professor, Yale University School of Medicine

Cloud P. Paweletz, Ph.D., Head, Translational Research Laboratory; Biomarker Lead, Belfer Institute for Applied Cancer Science, Dana Farber Cancer Institute

  • How to implement in a way that benefits patients
  • What information are you getting and how will people use it?
  • Who pays? Are we ready for plasma-based NGS tests?
  • Lessons learned

5:00 Reception with Exhibit and Poster Viewing

6:00 Close of Day

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Friday, March 11

7:00 am Breakfast Presentation: Tracking of Circulating Cell-Free DNA from Plasma for Treatment Response Monitoring

Raj Krishnan, Ph.D., CEO, Biological Dynamics, Inc.

Interest in the isolation, quantification, and analysis of cell-free biomarkers directly from blood has grown significantly. A proprietary platform has been developed for isolating and quantifying circulating biomarkers from physiological solutions using AC Electrokinetics (ACE). Biomarkers, such as high molecular weight cell-free DNA, have been established as indicators of tumor burden, and our TR(ACE) assay is currently being developed as a rapid, inexpensive method to follow treatment response in cancer patients.


7:55 Chairperson’s Remarks

Grace Zhao, Ph.D., Co-Founder and Director, Research, AccuraGen

8:00 An Ultra-Accurate System for Cancer Mutation Detection in Circulating Cell-Free DNA from Plasma

Grace Zhao, Ph.D., Co-Founder and Director, Research, AccuraGen

Rare mutation detection using circulating cfDNA presents two major challenges: low input, and relatively high error rate of current NGS technology. At AccuraGen, we have developed an innovative assay platform to amplify cfDNA, and correct sequencing error to enhance mutation detection at a high accuracy.  AccuraGen provides flexible liquid biopsy assays that cover from hundreds to handful of genes with a reliable detection rate of 0.05% in 5000 copies of genome.

8:30 High Sensitivity NGS Analysis of ctDNA: Applications to Non-Small Cell Lung Cancer and Beyond

Tim Forshew, Ph.D., Head, Technology Development, Inivata, Ltd.

It is now established that a broad spectrum of cancers release circulating tumor DNA (ctDNA) into the blood. Detection and quantification of this DNA has numerous potential clinical applications but raises challenges that need to be overcome. We published the first NGS method to detect mutations de novo through ctDNA sequencing (TAm-Seq) and will present the development of our optimized, highly sensitive multi-gene panel method, with supporting clinical data.

9:00 Multipanel Massive Parallel Sequencing cfDNA in Monitoring Cutaneous Melanoma Progression

Dave S.B. Hoon, Ph.D., Director, Molecular Oncology and Sequencing Center, John Wayne Cancer Institute, Providence Health Care

Analysis of cfDNA gene mutation panel in melanoma patients serial bleeds over several years of follow-up can be very informative on events ongoing during tumor progression. The highly sensitive and approach of multiple gene mutation panel assessment by MPS of cfDNA provides a very comprehensive analysis to allow correlation to real-time clinical events of patients. These retrospective studies demonstrate that cfDNA mutations can arise at different time points during tumor progression. This approach of precision medicine monitoring melanoma progression allows a more accurate real-time assessment of what is transpiring in the patient.

9:30 Measuring Donor-Derived Cell-Free DNA in Organ Transplant Recipients as a Dynamic Biomarker of Rejection

John J. Sninsky, Ph.D. CSO, CareDx

A clinical-grade NGS assay was developed to monitor donor-derived cell-free DNA (dd-cfDNA) in plasma from solid organ transplant recipients. Longitudinal samples from heart and kidney transplant patients show elevated dd-cfDNA levels prior to and at the time of acute rejection which are reduced following successful immunosuppressive therapy.

10:00 Presentation to be Announced

10:30 Coffee Break with Exhibit and Poster Viewing

11:00 Clinical Evidence for the Utility of the cobas® EGFR Mutation Test v2 with Liquid Biopsy Samples from NSCLC Patients

John Palma, Ph.D., Director, Medical Affairs, Roche

Common challenges to ascertaining EGFR mutation status in non-small cell lung cancer are the lack of or inadequacy of biopsy material. The cobas® EGFR Mutation Test v2 was developed to detect the most common mutations in exons 18-21, including T790M, for both tissue and plasma. Using different cutoffs for sample type, the detection of 42 mutations is now possible. While maintaining a high positive predictive value to detect EGFR mutations relative to tissue results, liquid biopsy testing could eventually enable the detection of acquired mutations during treatment.


11:30 Plasma Genotyping as a Novel Biomarker in Non-Small Cell Lung Cancer & Tool for Drug Development

Adrian G. Sacher, M.D., Clinical Fellow, Medicine, Dana-Farber Cancer Institute

Plasma genotyping of cell-free DNA (cfDNA) is quickly evolving as a method to select personalized therapy as well as monitor response to therapy in lung cancer. However, prospective data on the optimal platform and utility of plasma genotyping assays is limited. This talk will review the current state-of-the-art and present results from our ongoing prospective studies of plasma genotyping in lung cancer at the Dana-Farber Cancer Institute.

12:00 pm Quality Assessment of Cell-Free DNA to Guide Downstream Molecular Analyses

Muhammed Murtaza, Research Assistant Professor, Co-Leader, Center for Non-Invasive Diagnostics, Translational Genomics Research Institute

Recent proof-of-principle studies have demonstrated potential utility of sequencing cell-free DNA in cancer diagnostics. However, little is understood about the effect of fragment size distributions in plasma DNA on the performance of sequencing-based assays. We developed a multiplexed assay to perform one-step analysis of DNA quantity and integrity from minute amounts of cell-free DNA using picoliter droplet digital PCR. Our results were predictive of diversity and obtainable depth-of-coverage in next-generation sequencing libraries made from cell-free DNA samples.

12:30 Close of Symposium

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