Cambridge Healthtech Institute’s Fourth Annual

Circulating Cell-Free DNA

Overcoming Technical Challenges to Provide Clinical Solutions

February 23-24, 2017 | Moscone South Convention Center | San Francisco, CA
Part of the 24th International Molecular Medicine Tri-Conference


The development of noninvasive methods to detect and monitor tumors continues to be a bottleneck in oncology research. Circulating cell-free DNA shows great promise, but still requires improvements and additional research before it becomes standard practice. At Cambridge Healthtech Institute’s Fourth 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, monitoring treatment response, and moving cfDNA into clinical practice.

Thursday, February 23

7:00 am Registration and Morning Coffee


8:25 Chairperson’s Opening Remarks

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

8:30 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 sequencing-based method for ultra-sensitive and specific detection of circulating tumor DNA that is broadly applicable to different cancer types and clinical scenarios. 

9:15 Cell Free Tumor Derived DNA as a Diagnostic Tool for Human Malignancies

Chetan Bettegowda, M.D., Ph.D., Assistant Professor, Neurosurgery and Oncology, Johns Hopkins University School of Medicine

Neoplasms have been shown to shed cell free molecules of DNA into various biofluids. The detection and quantification of tumor-derived DNA (tDNA) in these biofluids can be exploited for diagnostic benefit. The applications of tDNA detection with regards to screening, diagnosis and disease monitoring will be discussed in a variety of cancer types.

10:00 Novel AC Electrokinetic Platform for Isolating Cell-Free DNA & Exosome Biomarkers for Clinical Applications

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

Biological Dynamics have developed a novel lab-on-a-chip AC Electrokinetics platform that offers a rapid and affordable way to isolate and quantify cell-free nanoparticles (cfDNA, proteins & exosomes) directly from biofluids, with the overall goal of improving precision medicine in oncology.

10:15 Improved Material for Developing, Validating, and Monitoring Liquid Biopsy Assays

Dale Yuzuki, MA, Med, Director, Market Development – Oncology, SeraCare Life Sciences

Random ultrasonication-based fragmentation methods have inherent weaknesses. Current needs for liquid biopsy assay development, validation, and monitoring include standards that are more commutable to native samples, highly multiplexed, and behave in library preparation close to native plasma ctDNA.

10:30 Coffee Break with Exhibit and Poster Viewing


11:15 Technological Challenges and Clinical Applications of ctDNA

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

Our group has developed an NGS-based assay that applies novel molecular and computational error suppression techniques to enable ultrasensitive measurement of ctDNA. Data will be presented from ongoing studies to establish the clinical utility of this technology, with a focus on monitoring of therapeutic response.

11:45 Liquid Biopsies in Precision Oncology

Filip Janku, M.D., Ph.D., Assistant Professor, Investigational Cancer Therapeutics (Phase I Program), MD Anderson Cancer Center

Unlike tissue biopsies, obtaining liquid biopsies such as samples of plasma-derived cell-free DNA is a minimally invasive approach. Plasma cell-free DNA can be used to assess molecular profile at different time points and provide valuable information about genetic changes that occur during the disease trajectory, as cancer progression is not a static process. In addition to identification of molecular targets for cancer therapy, molecular testing of cell-free DNA can provide additional information about prognosis, evaluate response to therapy, reveal disease progression or recurrence, and detect early emergence of molecular abnormalities that drive resistance to systemic therapy. Agreement rate between the molecular profile of cell-free DNA and archival tumor tissue is deemed to be acceptable and ranges from 70%-100%. Recently, both the European Medicines Agency and the United States Food and Drug Administration approved a PCR-based cell-free DNA test to detect EGFR mutations in NSCLC as an alternative to molecular testing of tumor tissue.

12:15 pm Digital PCR, a Highly Reproducible Method for the Detection of Rare Genetic Variants

Jim Hugget, Ph.D., Senior Lecturer, Analytical Microbiology, School of Bioscience and Medicine, Faculty of Health and Medical Science, University of Surrey

Digital PCR (dPCR) offers a potentially accurate method for the measurement of rare genetic variants using cell free DNA. This study investigated the performance of dPCR and evaluated its sensitivity and reproducibility, comparing 21 laboratories, when measuring KRAS mutations both as fractional abundance and absolute mutant copies.

12:30 Session Break

12:40 Luncheon Presentation: RainDance Technologies: Robust NGS Target Enrichment and Ultra-Sensitive Digital PCR to Profile & Monitor Mutations in Circulating cfDNA

Fraser Symmans, Ph.D., M.D., Professor and Director, Research Operations Department of Pathology, Anderson Cancer Center

Jennifer Jackson, Ph.D., Senior Scientist, RainDance Technologies

Hear how the only unified NGS target enrichment and digital PCR platform is enabling researchers to profile and monitor critical mutations in blood with an easier and faster workflow than before.

1:15 Session Break

1:50 Chairperson’s Remarks

Laura L. Elnitski, Ph.D., Principal Investigator, Genomic Functional Analysis, National Human Genome Research Institute

2:00 Featured Poster: Comprehensive Analysis of 13 Different Methods for Bisulfite Conversion of Circulating Cell-Free DNA

Mai-Britt Worm Orntoft, Student, Molecular Medicine, Aarhus University Hospital Skejby

Blood circulating cell-free DNA (cfDNA) is becoming a popular basis for novel biomarkers, and especially disease specific cfDNA methylation patterns have gained much attention. A significant challenge for the utilization of cfDNA methylation markers is the very limited amount of cfDNA present in blood that is reduced even further when cfDNA undergoes bisulfite conversion (BSC) prior to biomarker detection, which reportedly leads to significant cfDNA loss. Yet, only few efforts have focused on ensuring high cfDNA BSC efficiency and recovery, and few commercial kits are directed at this purpose. To identify the BSC method with the highest DNA recovery, this study compared 13 different methods, of which 6 are compatible with automation.


2:30 Clinical Applications of Liquid Biopsies: A Payer’s Perspective

Girish Putcha, M.D., Ph.D., Director, Laboratory Science, Palmetto GBA (MolDX)

Liquid biopsies in oncology hold great promise for multiple clinical applications, from screening and diagnosis to monitoring for residual disease or resistance to the selection of both targeted and immuno-oncology therapies. Each use case presents different opportunities and challenges for payers, which will be discussed.

3:00 Standardizing Blood Collection for cfDNA Detection by Sample Stabilization with the Cell-Free DNA BCT®

Landon Olp, Ph.D., Research & Development, Scientist, Immunology & Biomarkers, Streck

The Cell-Free DNA BCT stabilizes nucleated blood cells up to 14 days, improving sample collection/transport logistics while minimizing variability of cfDNA preparation.

 Natera3:15 Personalized Custom Panels for the Detection of Circulatory Tumor DNA Mutations

Bernhard Zimmermann, Ph.D., Senior Director, Research & Development, Natera

We have developed an approach to detect cancer signatures in plasma by ultra-deep sequencing of custom multiplex PCR assays to mutations found in the tumor. We demonstrate detection of clonal and subclonal mutations in treatment naïve lung cancer patients, of MRD and relapse up to one year before clinical manifestation.

3:30 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


4:15 KEYNOTE PRESENTATION: Novel Developments in Tracking Minor Fractions of Tissue and Tumor Epigenetic Signatures in Circulating-DNA

G. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School

Epigenetic marks in circulating DNA can be a powerful tool for tracking healthy tissue damage or for monitoring tumors during cancer therapy. Just as with mutated DNA, epigenetically altered DNA that provides clinically useful information is often masked by high excess of epigenetically ‘normal’ DNA. We present Methylation-Sensitive Nuclease-assisted Minor-allele Enrichment, MS-NaME, a simple and powerful approach that removes unaltered DNA in order to focus on clinically relevant DNA epigenetic changes. This single-step approach retains current sample preparation protocols almost unchanged and combines seamlessly with existing technologies like MS-HRM, Methylight and bisulfite sequencing. Application in clinical samples and liquid biopsies will be presented.

4:45 Peripheral Monitoring of Neurodegeneration Using cfDNA Methylation

Zac Chatterton, Ph.D., Postdoctoral Fellow, Neuroscience, Icahn School of Medicine, Mount Sinai

Neurodegeneration occurs in a variety of human diseases; however, molecular profiling of the brain is restrictive. Cell free DNA (cfDNA) derived from neurological tissue holds great promise for the detection and monitoring of neurodegeneration. Within our lab we exploit the unique DNA methylation profiles of brain cells to create molecular diagnostic assays capable of detecting peripheral neurological derived cfDNA.

5:15 Characterizing a DNA Methylation Locus of Pan-Cancer Importance for Use in Biofluid Diagnostics

Laura L. Elnitski, Ph.D., Principal Investigator, Genomic Functional Analysis, National Human Genome Research Institute

Cancer diagnostics is moving into noninvasive screening and rapid detection methods through the isolation of circulating tumor cells and circulating tumor DNA. We measured the magnitude of differential methylation of the ZNF154 CpG island in TCGA data and colon, lung, breast, stomach, and endometrial tumors and found all tumor types hypermethylated at this locus. As shown through experimental and computational analyses, this biomarker has demonstrated potential for blood-based cancer screening.

5:45 Reception with Exhibit and Poster Viewing

6:45 Close of Day

Friday, February 24

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Registration Open


8:25 Chairperson’s Remarks

Philip C. Mack, Ph.D., Associate Adjunct Professor, Internal Medicine, Hematology and Oncology, University of California, Davis Medical Center

8:30 Epigenetically Altered Circulating Nucleosomes - Validation of a New Diagnostic Approach for Colorectal Cancer

Jason Terrell, M.D., CMO, VolitionRx

In a retrospective training cohort of 4800 patients presenting with symptoms of Colorectal diseases generated a diagnostic NuQ® panel with sensitivity of 81% at a specificity of 80% in an age adjusted linear regression model for the detection of Colorectal cancer (CRC). In a subsequent pilot prospective study of 58 subjects, a sensitivity of 91% at 90% specificity was achieved for the detection of CRC. We present the results of a validation study in an independent cohort of symptomatic subjects for a novel NuQ® based CRC diagnostic test.

9:00 Building Evidence of Utility for cfDNA in Cancer Management

Phillip G. Febbo, M.D., CMO, Genomic Health, Inc.

Precision medicine in cancer care requires robust interrogation of an individual’s tumor to guide therapy. Circulating cell-free DNA often includes tumor DNA and can enable genomic analysis when tumor tissue is unavailable or difficult to obtain. However, important clinical and technological limitations need to be acknowledged and addressed in order to develop a valid test that has clinical utility for an intended patient population.

9:30 Are Liquid Biopsies Ready for Routine Clinical Use?

Philip C. Mack, Ph.D., Associate Adjunct Professor, Internal Medicine, Hematology and Oncology, University of California, Davis Medical Center

Detection of actionable genomic alterations is a requisite component for NCCN guideline-compliant work-up of several tumor types, including NSCLC adenocarcinoma. Moreover, identification of acquired resistance mutations emergent at time of progression on targeted therapies is practical and, in some cases, required for patients to receive next-generation agents. Liquid biopsy, including analysis of circulating tumor DNA (ctDNA), offers a non-invasive mutation genotyping option when traditional biopsies are not feasible. The reliability and clinical utility of this approach will be discussed.

10:00 Clinical Utility of Donor-Derived Cell-Free DNA in Transplantation

Robert Woodward, Ph.D., Senior Director, Research & Development, CareDx

AlloSure design, including judicious SNP selection, robust amplification strategy and a novel interpretative algorithm, enables accurate and reproducible clinical-grade results. Evidence supporting clinical validity and utility for multiple heart and kidney transplant indications will be described.

10:30 Coffee Break with Exhibit and Poster Viewing

11:15 Clinical Implementation of Digital PCR for Cancer Diagnostics and Monitoring

Alexander Dobrovic, Head/Group Leader, Translational Genomics, Olivia Newton-John Cancer Research Institute

This presentation will discuss digital PCR as a diagnostic and monitoring tool using liquid biopsies with insights from our clinical testing and research program.


11:45 Ultra-Sensitive Mutational Analysis in Cell-Free DNA by Digital PCR and NGS Technologies

Rachel Tam, Senior Scientific Researcher, Oncology Biomarker Development, Genentech

Circulating cell-free DNA (cfDNA) in plasma offers a non-invasive approach to monitor tumor molecular profiling in real-time at multiple time-points, detection of emerging genomic alterations associated with drug resistance and clarifying cancer prognosis and diagnosis of cancer recurrence or progression. We developed an ultra-sensitive droplet digital PCR (ddPCR) approach to detect actionable cancer biomarkers in cfDNA. We compared this ddPCR approach to other orthogonal technologies, including qPCR and NGS, and achieved 100% concordance across these platforms.

12:15 pm Applications of Plasma Genotyping for Advanced Non-Small Cell Lung Cancer

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

Through collaboration between thoracic oncologists and biomarker scientists at DFCI, we have spent the recent years developing approaches for targeted genotyping of plasma cell-free DNA in advanced NSCLC. Our approach primarily focuses on rapid assays for clinical application, including droplet digital PCR and targeted NGS assays. We will review our approach to clinical validation and present ongoing clinical investigations using these assays to study response and resistance to targeted therapies.

12:45 Close of Symposium

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