Cell-free DNA (cfDNA) is a relatively new technique with an exponential increase in applications for a variety of uses. The clinical utility of these new methods will be evaluated by thought-leaders in the field using the latest case studies. Non-invasive detection of cell-free DNA promises to impact clinical protocols and treatment regimens. cfDNA will determine the standard of care in oncology, transplant medicine and cardiovascular disease. This field is emerging as one of the most promising and exciting areas of medicine and has already made a huge impact on prenatal care.

Scientific Advisory Board - A Message from the Board Members
Luis A. Diaz, M.D., Associate Professor, Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Conference Chairman
Maximilian Diehn, M.D., Ph.D., Assistant Professor, Radiation Oncology, Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University
David S. B. Hoon, MSc, Ph.D., Chief of Scientific Intelligence, Director, Molecular Oncology, Director, JWCI Sequencing Center, John Wayne Cancer Institute

WEDNESDAY, AUGUST 19

10:30 Registration

12:40 pm Luncheon Presentation: Precision-Based Circulating Tumor DNA Detection in Gynecologic Cancer Patients

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

We developed a rapid and efficient approach for variant discovery in gynecologic cancers which couples tumor-specific mutation identification to digital PCR-based ctDNA detection. We generated tumor mutation profiles for each of our ovarian and endometrial cancer patients and tested this pipeline to detect and monitor tumor status. All results were compared against current FDA-approved biomarkers and the known clinical status of the patients, demonstrating the highly sensitive, specific and robust nature of our approach.

1:25 Refreshment Break in the Exhibit Hall with Poster Viewing

OPENING SESSION

1:50 Chairperson’s Opening Remarks

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

3:00 Blood-Based Genotyping of Colorectal Cancer Patients

Giulia Siravegna, MSc, Ph.D. Student, Molecular Medicine, Oncology, School of Medicine, University of Torino; IRCCS-Candiolo Cancer Institute

Liquid biopsy and cfDNA analysis allow genotyping of colorectal cancer (CRC) patients using a blood sample. CRC patients represent a model to assess whether blood analyses could in principle be used to perform diagnosis, to guide clinical decisions and to monitor the efficacy of therapies, establishing proof of principle that genotyping of cancer alleles in the patients’ blood allows clinically valuable longitudinal assessment for patients.

3:30 Urinary Circulating Free DNA Platform for Diagnosis and Cancer Treatment Monitoring

Vlada Melnikova, Ph.D., Vice President, Research and Development, Trovagene Inc.

The concept of liquid biopsies is now expanding to include urine as a specimen type. Using DNA extraction process that isolates systemic cfDNA and PCR-NGS enrichment method for mutation detection, we demonstrate high clinical sensitivity for detection of genomic alterations across different cancer types. Accurate quantitation using validated protocols reveals that longitudinal dynamics of mutational load in urine correlates with disease burden and drug response, thus enabling development of novel algorithms to inform treatment decisions.

4:00 Refreshment Break in the Exhibit Hall with Poster Viewing

NOVEL CLINICAL APPLICATIONS OF RARE MUTATION DETECTION TECHNOLOGY

4:35 Chairperson’s Introduction: PAP Smear Diagnostics for Endometrial and Ovarian Cancers

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

Dr. Diaz will introduce the topic and speakers of this session on novel clinical applications of rare mutation detection technology. He will also review findings from a study that demonstrates that DNA from most endometrial and a fraction of ovarian cancers can be detected in a standard liquid-based Pap smear specimen obtained during a routine pelvic examination.

4:45 Circulating Cell-Free DNA and Circulating Tumor Cells as Complementary Sources of Liquid Biopsy in Cancer Patients

Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf

Circulating cell-free DNA and genomic DNA amplified from single circulating tumor cells harbor complementary information on mutations relevant for the treatment of individual cancer patients. Here the technical challenges and clinical implications of both approaches are discussed in the context of cancer therapy in patients with solid tumors.

5:15 Cell-Free DNA in Transplant Medicine

Kiran K. Khush, M.D., MAS, Assistant Professor, Medicine, Cardiovascular Medicine, Stanford University

This presentation will review clinical applications of cell-free DNA testing in transplant medicine, specifically focusing on the non-invasive diagnosis of acute rejection, unbiased screening for pathogens, and measurement of overall level of immunosuppression. The focus will be on heart and lung transplantation, with illustrative cases.

5:45 Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Exome Sequencing of Blood-Derived DNA

Giulio Genovese, Ph.D., Computational Biologist, Stanley Center for Psychiatric Research, Broad Institute

Clonal expansion in blood is readily detected from whole-exome sequencing of DNA in peripheral-blood cells, it most frequently involves somatic mutations in genes DNMT3A, ASXL1, and TET2, and is often a precursor in blood malignancies. While uncommon before 50 years of age, we observe it in a cohort of 12,380 subjects in more than 10% of individuals above 65 years of age.

6:15 Close of Day

6:00 Dinner Short Course Registration

THURSDAY, AUGUST 20

TECHNOLOGY FOR PROFILING cfDNA

8:25 Chairperson’s Opening Remarks

Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf

8:30 Whole Genome Sequencing of Plasma DNA in Patients with Cancer

Michael R. Speicher, M.D., Department Chair, Institute of Human Genetics, Medical University of Graz

To scan the tumor genomes of patients with cancer noninvasively we establish a genome-wide copy number profile of the tumor by whole-genome sequencing from plasma at a shallow sequencing depth. In parallel, we sequence a panel of high-interest genes and introns with frequent fusion breakpoints with high coverage. Data of patients with breast, colon, and prostate carcinoma will be presented.

9:00 Diagnostic Applications of Cell-Free DNA in Solid Organ and Bone Marrow Transplantation

Iwijn De Vlaminck, Ph.D., Assistant Professor, Biomedical Engineering, Cornell University

This talk will cover applications of cell-free DNA in the diagnosis of rejection in solid-organ transplantation, and Graft Versus Host Disease in bone marrow transplantation, as well as applications of cell-free DNA monitoring in the broad, hypothesis-free monitoring of infection.  

 9:30 The Use of Multiplexed ICE COLD-PCR Coupled to Multiple Downstream Analysis Platforms for Detection of Low Level Sequence Alterations

Ben Legendre, Ph.D., Technical Director, Laboratory Operations, 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 many different downstream analysis platforms means that efficient detection of alterations at ≤0.01% in samples is feasible for most laboratories. Increased sensitivity using less DNA enables monitoring and detection of alterations in the low volumes of liquid biopsies for patient treatment, monitoring and surveillance.

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

LIQUID BIOPSY- Comparing and Contrasting Circulating Biomarkers

11:20 PANEL DISCUSSION

Moderator: Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf

Panelists:

Nitzan Rosenfeld, Ph.D., Senior Group Leader, CRUK-CI, University of Cambridge; CSO, Inivata, Ltd.

Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf

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

• Potential and pitfalls of current methods used for liquid biopsy (CTCs, ctDNA, miRNAs)

• Current areas of clinical applications of liquid biopsy (e.g., cancer screening, predicting outcome, monitoring therapies, discovering resistance mechanisms)
• Future developments required to move liquid biopsies into clinical management of cancer patients

•We will discuss the current challenges and future perspectives of CTCs and circulating nucleic acids (ctDNA, microRNA) as novel biomarkers in clinical oncology

12:20 pm Clinical Translation of cfDNA for Solid Organ Transplantation

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

For reimbursement, clinical translation of cfDNA for solid organ transplantation requires elevated levels of evidence (LOE). Examples of needed LOE that will be discussed include the rigor of implementation and maintained accuracy and reproducibility of a test in a CLIA laboratory and multi-center prospective trials for clinical validity and utility.

 12:35 Quantification of Circulating Biomarkers from Plasma and Serum Using AC Electrokinetics

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.  Biological Dynamics has developed proprietary platforms for isolating and quantifying large circulating biomarkers from physiological solutions using AC Electrokinetics (ACE).  Biomarkers, such as necrotic cell-free DNA (ncfDNA), have been established as indicators of cancer, and the ability to detect and track these biomarkers unlocks a new era in early disease diagnosis and treatment response monitoring.

  12:50 Luncheon Presentation: Clinical Experience Using EGFR Mutational Analysis in ctDNA and PDL-1 and c-MET in CTCs in the Treatment of Patients with Lung Adenocarcinoma

Lyle Arnold, Ph.D., Senior Vice President R&D, CSO, Biocept

Hatim Husain, M.D., Assistant Professor, Medicine, UCSD Moores Cancer Center

Liquid biopsies offer the opportunity to interrogate a number of different target sample types, including ctDNA and CTCs. At Biocept both ctDNA and CTCs are used for identifying medically actionable biomarkers to assist in the optimal treatment of patients.  We will report on the combined use of PDL-1, c-MET, and EGFR mutation status in the treatment selection and monitoring of patients with lung cancer.

1:20 Session Break

CLINICAL APPLICATIONS IN ONCOLOGY

2:00 Chairperson’s Remarks

Maximilian Diehn, M.D., Ph.D., Stanford University

2:05 An Ultrasensitive Method for Quantitating Circulating Tumor DNA with Broad Patient Coverage

Maximilian Diehn, M.D., Ph.D., Assistant Professor, Radiation Oncology, Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University

This presentation will review the potential clinical utility of ctDNA analysis using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq), a novel next-generation sequencing-based approach for ultrasensitive ctDNA detection. Applications of CAPP-Seq for the personalization of cancer detection and therapy are discussed.

2:35 Personalized Cancer Patient Monitoring with Plasma DNA Multimarker Analysis

Alain R. Thierry, Ph.D., Senior Investigator, Research Institute in Oncology of Montpellier, INSERM

Based upon crucial observations on the structure and origins of circulating cell free DNA (cfDNA), we designed a specific method to analyze five different biomarkers on plasma DNA. Point mutation detection was the subject of the first clinical validation of the cfDNA analysis in oncology in a study on KRAS and BRAF mutation testing in metastatic colorectal cancer patient. We demonstrated that quantitative markers such the total cfDNA concentration, the mutant cfDNA concentration, the cfDNA mutation load and a fragmentation index are all strong prognostic factors. Lastly, we showed that point mutations initially at very low allele frequency (<0.1% in cfDNA) may confer resistance under subsequent targeted therapy suggesting the need for highly sensitive methods for theragnostics purpose as well as for patient follow up.

3:05 Circulating Tumor DNA (ctDNA) as a Non-Invasive Substitute to Metastasis Biopsy for Tumor Genotyping and Personalized Medicine in a Prospective Trial across All Tumor Types

Jean-Yves Pierga, M.D., Ph.D., Circulating Cancer Biomarkers Lab, SiRIC, Translational Research and Medical Oncology, Institut Curie and
University Paris Descartes

ctDNA analysis was an alternative to invasive biopsy of metastasis, irrespective of cancer type and metastatic site, for multiplexed mutation detection in a prospective Phase II trial in patients with different tumor types. This could allow selecting appropriate and optimal therapies based on the context of a patient’s tumor genetic content.

3:35 Circulating Plasma Tumor DNA as a Biomarker for Individualized Medicine in Early Stage Breast Cancer

Ben H. Park, M.D., Ph.D., Associate Professor, Oncology, Johns Hopkins University

Circulating plasma tumor DNA (ptDNA) could be used as a marker of minimal residual disease after surgery for early stage breast cancer. Using droplet digital PCR, we demonstrate that ptDNA can be detected preoperatively with 93.3% sensitivity and 100% specificity, and ptDNA can be detected postoperatively in patients without evidence of disease. The ability to use this information for clinical decision-making will be discussed.

4:05 Close of Conference