Cambridge Healthtech Institute’s Second Annual

Circulating Cell-Free DNA

Pushing the Limits of Early Detection

February 19-20, 2015 | The InterContinental San Francisco | San Francisco, CA
Part of the 22nd International Molecular Medicine Tri-Conference


About this Conference:

Circulating nucleic acids are an important emerging biomarker in cancer diagnostics as well as a non-invasive diagnostic solution for a wide range of clinical disorders. Cambridge Healthtech Institute's Second Annual Circulating Cell-Free DNA will cover clinical, technical, and biological aspects of both cfDNA and cfRNA. In addition to exploring applications in cancer, this event will assess existing detection technologies and showcase novel approaches for rare event and minimal residual disease detection.

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Thursday, February 19

7:30 am Registration and Morning Coffee


9:00 Chairperson’s Opening Remarks

Dave Hoon, Ph.D., Director & Professor, Molecular Oncology, John Wayne Cancer Institute


Detection of Circulating Tumor DNA in Early and Late Stage Human Malignancies

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

Cancer cells shed cell free, tumor specific DNA (ctDNA) into various body fluids. These molecules of DNA harbor genetic alterations that can be harnessed for diagnostic purposes. Using next generation sequencing based approaches, we have been able to detect ctDNA in a large number of advanced and localized malignancies. This suggests that ctDNA has the potential to act as a personalized biomarker for individuals with cancer.

9:40 cfDNA Ultra-Rare Allele Detection and Discovery

Seth D. Crosby, M.D., Director, Partnerships, Genetics, Washington University

We are currently working on methods to both detect known mutations and discover new ones in cell-free plasma DNA.

10:10 Future Clinical and Research Applications of Circulating Tumor DNA

Luis A. Diaz, M.D., Associate Professor, Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center

An overview of ctDNA for clinical and research applications with a critical review of the limitations and potential of this technology based on the biology of this novel biomarker.

10:40 Coffee Break with Exhibit and Poster Viewing


11:15 Evaluation of EGFR Mutations in Plasma from NSCLC Patients: Utility in Managing Patients on TKI Therapy

Mitch Raponi, Ph.D., Senior Director, Molecular Diagnostics, Clovis Oncology

We are utilizing blood-based molecular testing to determine resistance mutation profiles in these patients with the goal of enabling targeted subsequent therapy without need for repeat lung biopsy. The utility of plasma-based EGFR mutational analysis will be described in the context of CO-1686, a novel third-generation TKI that selectively inhibits the EGFR activating and T790M resistance mutations in NSCLC patients.

11:45 Serial Monitoring of EGFR Mutations in Plasma and Matched Tissue from EGFR Mutant Non-Small Cell Lung Cancer Patients on Erlotinib

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

We report on the detection, quantification and monitoring of EGFR mutations by droplet digital PCR in cfDNA on a prospective clinical trial of EGFR-mutant NSCLC patients on erlotinib. Our results strongly suggest that cfDNA genotyping has clinical utility in the molecular assessment of patients at diagnosis, and providing molecular understanding of patient’s tumor evolution.

12:15 pm Circulating Cell-Free Necrotic DNA as a Tool for Monitoring Treatment Response in Cancer Patients 

Rajaram Krishnan, Ph.D., CEO, Bioengineering, Biological Dynamics, Inc.

 Quantification of cell-free necrotic DNA (cfnDNA) from plasma and serum has great potential for predicting remission, stable and progressing disease in cancer. Biological Dynamics has developed a technique to rapidly quantify cfnDNA in plasma and serum. We report the results of a longitudinal study across multiple cancer types.  

12:30 Session Break

12:40 Luncheon Presentation: Detecting Circulating Tumor Cells by Fluid Biopsy and Profiling Somatic Tumors with Next-Gen DNA Sequencing

Darren Link, Ph.D., Co-founder and CTO, Research and Development, RainDance Technologies Inc.

Novel, non-invasive Fluid Biopsy™ research applications are transforming cancer research by enabling more accurate, reliable, and early detection of circulating tumor DNA in plasma. Hear how new Next-Gen DNA Sequencing technology is being deployed to rapidly detect and cost-effectively profile informative driver mutations and how ultra-sensitive Digital PCR technology is being applied to monitor minimal residual disease and for precise follow-up mutation validation, all from a simple blood test.

1:15 Session Break


1:50 Chairperson’s Remarks

2:00 Tracking Changes in Circulating Tumor DNA in Patients with Non-Small Cell Lung Cancer

Abhijit A. Patel, M.D., Ph.D., Assistant Professor, Department of Therapeutic Radiology, Yale University School of Medicine

An ultrasensitive, multi-target assay will be presented that can identify and quantify mutant ctDNA using error-suppressed next-generation sequencing. This assay is able to monitor treatment response and disease progression in patients with non-small cell lung cancer, without prior knowledge of the mutation profile of their tumor.

2:30 Clinical Evaluation of cfDNA and Exosomes as Oncology Biomarkers

Shidong Jia, Ph.D., Scientist, Genentech

The enumeration and characterization of circulating tumor cells (CTCs), exosomes and circulating tumor-free DNA (ctDNA) in the peripheral blood may provide important prognostic and diagnostic information and might help to monitor efficacy of therapy. Specific examples will be shown to demonstrate the opportunities and challenges for the development of blood-based clinical diagnostics.

3:00 Refreshment Break with Exhibit and Poster Viewing

3:30 Enhanced Detection of Low-Level DNA Mutations Using Multiplexed ICE COLD-PCR Coupled to NGS or ddPCR

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

The use of “liquid biopsies”, where limited or no tumor tissue is available, is increasingly important for molecular demographics, diagnostics and pharmacodynamic monitoring of patients during therapy. The combination of MX-ICP with NGS and ddPCR platforms means that they can be used efficiently for detection of alterations at ≤0.01% in samples with <100 ng DNA. This enables monitoring and detection of alterations in the low volumes of liquid biopsies for patient treatment, monitoring and surveillance.

4:00 Clinical Utility of a Novel Approach of Digital Sequencing Assessment of Circulating Cell-Free DNA in Melanoma Patients

Dave Hoon, Ph.D., Director & Professor, Molecular Oncology, John Wayne Cancer Institute

We have developed a novel digital sequencing approach of cell-free circulating DNA with Guardant Health to monitor melanoma patients during treatment. The approach is novel in that complete exons of genes in circulation are sequenced for detection of mutations and deletions. The coverage is at >500x. Comparison of respective tumor biopsy and blood of patients shows the high concordance of the results (>90%). The novel approach provides a highly comprehensive analysis of cell-free circulating genomic DNA in cancer patients.

4:30 Use of Non-Invasive Tumor Sequencing Assay on Patients with Advanced Cancers and its Clinical Utility

AmirAli Talasaz, Ph.D., President & CTO, Guardant Health, Inc.

Analysis of genomic alterations in advanced malignant disease is quickly becoming the standard of care in oncology. GUARDANT360, a blood-based liquid biopsy approach that analyzes circulating tumor DNA (ctDNA), offers a simple and comprehensive tool for real-time tumor genetic profiling in advanced refractory cancer patients.

5:00 Personalized Cancer Surveillance and Recurrence Detection in Gynecologic Malignancies

John A. Martignetti, M.D., Ph.D., Genetics and Genomic Sciences, Pediatrics, Obstetrics/Gynecology & Reproductive Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai

The majority of patients with ovarian cancer who demonstrate a “complete clinical response” by current surveillance methods actually harbor residual disease and almost all will die from their disease. Using ddPCR, we have developed a pipeline for generating highly sensitive and specific ctDNA biomarkers based upon WES and RNASeq of each patient’s tumor as part of a personalized cancer program and have begun assessing clinical utility.

5:30 Close of Day

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Friday, February 20

8:00 am Morning Coffee


8:25 Chairperson’s Remarks

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

8:30 Challenges in Measuring Circulating Nucleic Acids

Kai Wang, Ph.D., Principal Scientist, Institute for Systems Biology

Circulating nucleic acids have gained significant interest due to their potential diagnostic applications. The development of NGS platforms provides an opportunity to access a comprehensive profile of circulating nucleic acids. Some circulating DNA species have already been used in clinic; however, there are a number of challenges to accurately measuring levels of specific cell free nucleic acids especially for low concentration RNA sequences. However there is a great potential to use the spectrum of circulating nucleic acids to reflect specific physiopathological conditions.

9:00 Isolation of Circulating MicroRNAs from Microvesicles Found in Human Plasma

Pamela B. Cassidy, Ph.D., Research Associate Professor, Dermatology, Oregon Health and Science University

The remarkable stability of circulating miRNAs makes them excellent candidates for biomarkers in diagnostics and therapeutics. We describe a convenient method for the use of ExoQuick, a proprietary resin developed by Systems Biosciences, whereby microvesicles can be purified under gentle conditions using readily available laboratory equipment. This protocol provides a convenient method for identifying potential disease-specific biomarkers in biological fluids including serum and plasma.


9:30 Detecting Hypomethylation and Point Mutations in Circulating Cell-Free DNA

Timothy Harkins, Ph.D., Executive Vice President, Development, Swift Biosciences

Deep sequencing using next generation sequencing (NGS) of circulating cell-free DNA (cfDNA) has shown that tumor specific mutations can be detected, providing an effective means to monitor disease, and treatment efficacy.  We have developed a pair of NGS assays that are cost effective, sensitive, and specific to assess the global methylation status of cfDNA with as few as 10 million sequencing reads or detect 1000’s of point mutations across oncogenes.

10:00 Detection and Quantitative Monitoring of ctDNA Mutation Status in Cancer Patients

Vlada Melnika, Ph.D., Vice President, Research & Development, Trovagene, Inc.

An optimized isolation technique for cell-free DNA makes it possible to detect systemically derived cfDNA both in plasma and urine. Using a small footprint capture and enrichment technique, we demonstrate the analytical detection and quantification of these tumor fragments down to sensitivity of less than 0.01%, creating a non-invasive cancer mutation detection platform. Demonstrated correlation with tumor burden, drug response and disease progression supports clinical utility of precision cancer monitoring.

10:30 Coffee Break with Exhibit and Poster Viewing

11:00 Measuring Circulating Tumor DNA in Plasma By Picoliter Droplet-Based PCR For Colorectal Cancer Patient Follow-Up

Géraldine Perkins, M.D., Ph.D., Senior Consultant, GI Oncology, Georges Pompidou European Hospital, INSERM

Co-Authors: Garlan F., Didelot A. , Perkins G., Rice N., Zaanan A., Laurent-Puig P. and Taly V.

By combining microfluidic systems and clinical advances in molecular diagnostic, picoliter droplet-based digital PCR allows performing millions of single-molecule PCR in parallel to detect and quantify a minority of mutant sequences within a high quantity of non-mutated sequences with a sensitivity unreachable by conventional tools. Our presentation will illustrate the pertinence of this procedure for cancer research with a focus on its application for treatment efficiency follow-up and cancer recurrence by monitoring of circulating tumor DNA.

11:30 Next-Generation Sequencing of Methylated Free Circulating DNA to Develop a Blood-Based Biomarker for Ovarian Cancer

Kristina Warton, Ph.D., Senior Research Officer, Cancer, University of New South Wales and Kinghorn Cancer Centre, Garvan Institute

Free circulating DNA (fcDNA) studies often require analysis of clinical samples with limited or very low DNA concentrations. We have addressed the technical issues this raises by developing modified protocols for the purification of fcDNA from plasma, followed by MethylMiner MBD-2 capture of the methylated fraction and Next-Generation Sequencing. We present the data in the context of developing a blood-based methylation biomarker for ovarian cancer.

12:00 pm Rapid Isolation and Detection of Circulating Cell Free DNA/RNA Biomarkers for Cancer and Other Clinical Diagnostics

Michael J. Heller, Ph.D., Professor, Nanoengineering & Bioengineering, University of California San Diego

We have now demonstrated the rapid isolation and detection of circulating cell free DNA and RNA from a number of different hematological and solid tumor samples. Using AC dielectrophoretic (DEP) microarray devices, ccf-DNA/RNA can be isolated and detected by fluorescence within 10-15 minutes from small volumes (20ul-100ul) of patient blood, plasma and serum samples. Subsequent PCR and DNA sequencing analysis produces analytical results comparable to conventional sample preparation “gold-standard“ procedures which require considerably more time, effort, cost, as well as larger sample volumes.

12:30 Close of Symposium

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