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2014 Archived Content

Cambridge Healthtech Institute’s Inaugural
Circulating Cell-Free DNA
Advancing Non-Invasive Diagnostics
Part of the 21st Annual Molecular Medicine Tri-Conference

February 13-14, 2014 | Westin St. Francis | San Francisco, CA

Circulating cell-free DNA's most obvious applications are in cancer detection and monitoring. However, it also provides a non-invasive diagnostic solution for a wide range of clinical disorders. Cambridge Healthtech Institute's Inaugural Circulating Cell-Free DNA symposium will examine applications in cancer, prenatal diagnostics, cardiovascular disease and organ transplant monitoring. Molecular counting technologies, including digital PCR and next-generation sequencing, will be evaluated and new technologies and techniques will be showcased. Special focus will be given to clinical case studies to further explore the applications and potential of circulating cell-free DNA in diagnostics.

Day 1 | Day 2Symposia Brochure | Full Event Brochure  

Thursday, February 13

7:30 am Registration and Morning Coffee


9:00 Chairperson’s Opening Remarks

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


Plasma DNA Sequencing for Noninvasive Prenatal Testing and Cancer Detection

Dennis Lo, M.D., Ph.D., Director, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong

Over the last 5 years, there is much interest in the use of massively parallel sequencing of plasma DNA for molecular diagnostics. Hence, fetal chromosomal aneuploidies, genome-wide molecular karyotyping and even fetal whole genome sequencing have been accomplished through the sequencing of maternal plasma DNA. We have also shown that this approach can be used for the noninvasive detection of tumor-associated copy number aberrations and single nucleotide mutations in cancer patients.

9:35 Detecting Oncogenic Mutations from Circulating Tumor DNA (ctDNA): Lessons Learned from ctDNA Analysis in Clinical Trials

Elizabeth Punnoose, Scientist, Oncology Biomarker Development, Genentech

ctDNA is an attractive alternative to patient tumor biopsies to detect oncogenic mutations. Its value is in complementing tumor-based analysis to determine patients' current mutation status, longitudinal monitoring on treatment, as well as detection of resistance mutations as they arise. Results from ctDNA analysis from clinical trials of targeted agents will be discussed.

10:05 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.

10:35 Coffee Break with Exhibit and Poster Viewing

11:05 Circulating Tumor DNA for Noninvasive Cancer Diagnostics

Dana Tsui, Ph.D., Postdoctoral Research Fellow, Rosenfeld Lab, Cancer Research UK Cambridge Institute, University of Cambridge

This talk will review applications of circulating tumor DNA as a “liquid biopsy” to monitor cancer dynamics. Clinical cases will be presented to demonstrate the potential to monitor cancer patients’ response to treatment, and to identify de novo genomic changes that are linked to drug resistance. Practical considerations associated with the clinical implementation of circulating tumor DNA analysis will also be discussed.

11:35 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.

12:05 Detection and Monitoring of BRAF and KRAS Mutations in Cell-Free Urinary DNA of Metastatic Cancer Patients

Cecile Rose Vibat, Ph.D., Senior Director, Translational Science & Clinical Affairs, Trovagene

Detection and monitoring of oncogenic mutations in cell-free urinary DNA opens the possibility of a new paradigm for a truly non-invasive method of individualized care for metastatic cancer patients, which would enable the quantitation of mutational tumor load and respective concordance to therapeutic responsiveness followed by detection of emerging genomic alterations underlying acquired resistance. Next-generation sequencing techniques enable monitoring of key driver mutations and resistance mechanisms using targeted gene panels.

12:35 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:05 Session Break


1:50 Chairperson’s Remarks

Subhashini Chandrasekharan, Ph.D., Assistant Research Professor, Institute for Genome Sciences & Policy, Duke University


Sponsored by

Ariosa Diagnostics

1:55 Fetal Cell-Free DNA: How the Fraction and Amount Informs a Non-Invasive Prenatal Test Result

Arnold Oliphant, Ph.D., CSO, Ariosa Diagnostics

Cell free plasma DNA can be highly variable. Maternal factors, shipping, handling and laboratory processing can all have an influence on the plasma DNA that is evaluated for NIPT testing. It is important to evaluate these effects in each sample to assure that NIPT results provide added value to the patient.

2:10 Commercialization of Noninvasive Prenatal Testing: Ethical and Policy Implications

Subhashini Chandrasekharan, Ph.D., Assistant Research Professor, Institute for Genome Sciences & Policy, Duke University

The introduction of current and emerging noninvasive prenatal testing (NIPT) into clinics in the US and abroad raises both practical and ethical challenges. This talk will briefly discuss ethical, legal, social and practical issues associated with commercialization of NIPT technologies and their policy implications.

2:40 High Risk Screening and Outlook for the Future

Kumar Duraiswamy, M.D., MBA, Associate Director, Field Medical Affairs, Illumina, Inc.

In this talk, we examine the sequencing technologies that provide the framework for noninvasive prenatal testing (NIPT). This presentation will also compare and contrast the commercially available noninvasive prenatal tests in the United States, discusses clinical implementation recommendations from professional societies and highlights considerations for genetic counseling.

3:10 Refreshment Break with Exhibit and Poster Viewing

3:40 Initial Commercial Results from a Noninvasive Prenatal Aneuploidy Test that Employs Massively Multiplexed Targeted PCR Amplification and Sequencing of 19,488 SNPs

Matthew Hill, Ph.D., Vice President, Research, Natera, Inc.

Targeting tens of thousands of SNPs represents a significant advance over shotgun methods used to noninvasively detect fetal chromosome copy number abnormalities. This versatile platform generates array-like capabilities from PCR and NGS, yielding highly quantitative data to which robust Maximum Likelihood Estimation methods can be applied. We report here very high sensitivity and specificity achieved using this method, and its adaptation for detection of microdeletions in ccfDNA and other mixed samples.

4:10 Noninvasive Personalized Genomics

Charles R. Cantor, Ph.D., CSO, Sequenom

Cell-free DNA in plasma reflects cell death in a variety of host compartments. Differences in sequence, copy number or epigenetics among these compartments can be used to access DNA samples without invasive procedures. Depending on the application the circulating DNA can be analyzed by random shotgun sequencing, targeted sequencing, DNA mass spectrometry or PCR. Some examples of clinical applications of these approaches will be described.

4:40 Breakout Discussions

These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.

Next Steps for Noninvasive Prenatal Diagnostics

Moderator: Matthew Hill, Ph.D., Vice President, Research, Natera, Inc.

  • What are the existing technologies and how will NIPT evolve as the technology changes?
  • How should NIPT be implemented in a clinical setting?
  • How can higher sensitivity and specificity be achieved?

Using ctDNA in Clinical Trials

Moderator: Elizabeth Punnoose, Scientist, Oncology Biomarker Development, Genentech

  • Has the time come for using NGS for ctDNA analysis in clinical trials - what are the pros and cons?
  • Are technologies sufficiently mature for a ctDNA based companion diagnostic assay? If so which technology?
  • Can ctDNA levels be used for disease monitoring and as a surrogate for PFS similar to the use of MRD in leukemias?
  • Are we ready to replace tissue based mutation detection with ctDNA for routine use in clinical trials? What do we know and what do we still need to understand?

Circulating Cell-Free microRNAs

Moderator: Muneesh Tewari, M.D., Ph.D., Human Biology, Fred Hutchinson Cancer Research

5:25 Close of Day

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