Cambridge Healthtech Institute’s Eighth Annual

Cancer Molecular Markers

Guiding Cancer Management

February 16-18, 2015 | Moscone North Convention Center | San Francisco, CA
Part of the 22nd Annual Molecular Medicine Tri-Conference


The use of cancer biomarkers has gained an essential role in the treatment, monitoring and management of cancer. Staying up to date on the variety and use of biomarkers that is growing every year is becoming increasingly difficult. In its eighth year, this meeting will look at trends in discovering and validating cancer biomarkers to improve the efficacy of tumor targeting and bring them into powerful application in the clinic.

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Monday, February 16

10:30 am Conference Program Registration


11:50 Chairperson’s Opening Remarks

Stefanie Jeffrey, M.D., John and Marva Warnock Professor, Surgery; Chief of Surgical Oncology Research, Stanford University School of Medicine and Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University, Medical Center Hamburg-Eppendorf, University of Hamburg

12:00 pm CTC: Current Clinical Utility and Future Prospects

Jeffrey Smerage, M.D., Ph.D., Clinical Associate Professor, Division of Hematology and Oncology, University of Michigan

CTC enumeration is clearly associated with poor prognosis in several epithelial malignancies. A prospective randomized clinical trial in metastatic breast cancer (S0500) demonstrated that failure to clear CTC harbors a terrible prognosis, but that switching to a different chemotherapy is of no value. Future studies will focus on molecular characterization of CTC and investigating genomic, targeted therapies based on these results.

12:30 Qualifying Blood-Based Molecular Assays for Targeted Therapies in Cancer

Daniel C. Danila, M.D., Assistant Attending, Medicine, Memorial Sloan Kettering Cancer Center

Unmet needs in cancer drug development and patient management are the ability to monitor treatment benefit and to identify the target of interest in a tumor at the time treatment is being considered. Given the effort and cost to new blood biomarkers, it is essential to develop metrics to determine which promising assays warrant prospective testing in large-scale phase III trials to establish qualification in the context of use.

1:00 Session Break

1:15 Luncheon Presentation: High Sensitive Detection of Circulating Tumor Cells Including EMT-CTCs in NSCLC Patients by TelomeScan F35

Shinsaku Togo, M.D., Ph.D., Associate Professor, Division of Respiratory Medicine, Faculty of Medicine & Graduate School of Medicine, Juntendo University

We established a unique CTC-detecting platform using TelomeScan F35, a telomerase-specific replication-selective adenovirus expressing GFP. In clinical feasibility studies, we demonstrated that TelomeScan F35 is useful to detect alive and EMT-induced CTCs from patients of various types of cancer. In NSCLC, CTCs were sensitively detected from patients with early clinical stage (Stage I) and it suggests TelomeScan F35 is a powerful surrogate indicator and liquid biopsy for cancer diagnosis.

1:45 Session Break



2:30 Chairperson’s Remarks

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

2:40 Circulating Tumor Cells in Lung Cancer, Biomarkers, Biology, and Mouse Models

Caroline Dive, B.Pharm, Ph.D., Professor & Senior Group Leader, Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute

Dr. Dive will discuss the current utility of CTCs in lung cancer in early clinical trials and the challenges associated with use of new marker independent CTC enrichment platforms in clinical trial samples. She will also focus on the development of patient derived CTC explant models that now offer unique opportunities to study lung cancer biology, discover new drug targets, understand drug resistance mechanisms and test novel therapies.

3:10 Novel Approaches to Enable Molecular Characterization of CTCs

Nikolas H. Stoecklein, M.D., Professor, General Visceral and Pediatric Surgery, University Hospital of the Heinrich-Heine, University of Düsseldorf

The talk will cover a recently established workflow to enable high-resolution genomic analysis of single CTCs and will discuss the concept of diagnostic leukapheresis (DLA) to increase the detection rate of CTCs by screening larger blood volumes.

3:40 Deep Sequencing of Circulating Tumor Cells as a Window into Disseminated Cancer

Jens Lohr, M.D., Ph.D., Instructor in Medicine, Medical Oncology, Cancer Program, Dana-Farber Cancer Institute; Broad Institute

We have developed targeted and whole exome sequencing frameworks to explore the genomics of circulating tumor cells (CTCs), with a focus on defining somatic mutations in single CTCs. We are investigating how the genetics of CTCs evolve over time and how they compare to primary tumors and metastases.

4:10 Characterization and Molecular Profiling of CTCs using DEPArray™ and Ampli1™ Technologies

Farideh Z. Bischoff, Ph.D., Executive Director, Scientific Affairs, Silicon Biosystems

DEPArray™ allows sorting and recovery of target cells using image-based identification of specific markers. Enriched cell suspensions can be used to recover rare cells with 100% purity. Using this approach, CTCs have been successfully recovered for downstream molecular profiling and NGS.

4:25 Clinical Impact and Future Developments of Circulating Cancer Cells 

Patrizia Paterlini-Brechot, M.D., Ph.D., Professor, University Paris Descartes, Inserm Unit 1151 and Rarecells Diagnostics SAS

Circulating Cancer Cells are tumor cells which are extracted from blood without any bias and identified through a diagnostic approach,  cytopathology. They are the basis for clinical and molecular studies avoiding the classical troubles which affect Circulating Tumor Cells.

4:40 Break and Transition to Plenary Session

5:00 Plenary Session Panel 

6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing

7:30 Close of Day

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Tuesday, February 17

7:00 am Registration and Morning Coffee

8:00 Plenary Session Panel 

9:00 Refreshment Break in the Exhibit Hall with Poster Viewing


10:05 Chairperson’s Remarks

Stefanie Jeffrey, M.D., John and Marva Warnock Professor, Department of Surgery, Chief of Surgical Oncology Research, Stanford University School of Medicine

10:15 Platforms for CTC Isolation and Analysis

Z. Hugh Fan, Ph.D., Professor, Mechanical and Aerospace Engineering, University of Florida

We will present our recent results on integrating aptamers, antibodies, nanoparticles, and multivalent binding mechanisms with microfluidics for the isolation of cancer cells, as well as on the correlation between CTC enumeration and therapy responses of pancreatic cancer patients. Other platforms for CTC isolation and analysis will be reviewed and examined. Parameters for platform comparison will be discussed.

10:45 Circulating Tumor DNA:  Opportunities and Challenges on the Road to Clinical Utility

Mark Lee, M.D., Ph.D., Google[x] Life Sciences

The advent of new technologies for sensitive and specific detection of cell-free, circulating tumor DNA (ctDNA) in plasma has generated considerable enthusiasm for this new class of biomarkers to improve clinical decision-making in oncology.  Emerging evidence suggests a number of promising potential clinical applications.   Considerations and strategies to establish clinical utility of ctDNA will be discussed.

11:15 Biology and Function of Exosomes

Raghu Kalluri, M.D., Ph.D., Professor & Chair, Cancer Biology, MD Anderson Cancer Center

The lecture will discuss the biology and function of exosomes in cancer detection and progression of cancer. DNA, RNA and protein profiles will be discussed with specific emphasis on early detection of cancer.

11:45 Microfluidic Isolation of Microvesicles and Circulating Tumor Cells from Cancer Patients

Shannon L. Stott, Ph.D., Assistant Professor, Medicine, Massachusetts General Hospital and Harvard Medical School

Circulating tumor cells (CTCs) and microvesicles (MVs) are found in the bloodstream of cancer patients and have the potential to help guide cancer treatment. Through a collaborative effort between bioengineers, biologists, and clinicians, our group at MGH has developed microfluidic devices to isolate these rare circulating biomarkers from whole blood. I will describe our recent efforts to molecularly characterize CTCs and MVs, and the insights gained from our analysis.

12:15 pm Session Break

12:25 Luncheon Presentation I: Circulating Tumor Cells: From Enumeration to Comprehensive Characterization

Nicholas C. Dracopoli, Ph.D., Vice President, Oncology Translational Research, Janssen R&D, Johnson & Johnson

This presentation will describe a novel platform for the capture and analysis of circulating tumor cells (CTC). The platform is antibody independent and delivers viable CTCs in suspension. This novel platform enables routine enumeration of all tumor derived cells, ex vivo propagation of the CTCs, and comprehensive molecular and protein analyses using single cell analytical methods to characterize tissue of origin, epithelial-mesenchymal transition, stem cells and functional biomarkers.

12:55 Luncheon Presentation II: Exosomes and cfDNA: Complete Nucleic Acid Analysis from a Liquid Biopsy

Johan Skog, Ph.D., CSO, Exosome Diagnostics

Detection of circulating nucleic acids in the blood allows longitudinal monitoring of cancer patients, but any diagnostic test that uses biofluids needs a platform to maximize the capture of mutations. Plasma contains two cell-free sources of nucleic acids: cfDNA, generated from dying cells, and exoRNA enclosed in exosomes, which are actively secreted by cells in the body. The amount of nucleic acids in biofluids is limited, so co-isolation of exoRNA and cfDNA out of plasma maximizes sensitivity of detection.

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


2:00 Chairperson’s Remarks

Daniel H. Farkas, Ph.D., HCLD, FACB, Laboratory Director, Sequenom Center for Molecular Medicine

2:10 Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease

Atul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital; Co-Founder, Personalis and NuMedii

Dr. Butte’s lab at Stanford builds and applies tools to translate more than a trillion points of molecular, clinical, and epidemiological data -- measured by researchers and clinicians over the past decade and now commonly called “big data”-- into diagnostics, therapeutics, and new insights into disease. Dr. Butte will highlight his lab’s work on using publicly-available molecular measurements to discover new diagnostics and treatment mechanisms for type 2 diabetes and the evaluation of patients presenting with whole genomes sequenced.

2:40 Adventitious Maternal Cancer Detection during Non-Invasive Prenatal Testing of Circulating Fetal DNA

Nilesh Dharajiya, M.D., Director, Clinical Lab, Sequenom Laboratories 

Non-invasive prenatal testing of cell free DNA (cfDNA) provides a novel tool to detect chromosomal abnormalities prenatally. Maternal cfDNA is also sequenced, and therefore, we may learn about the mother’s genome or other medical conditions. Here, we provide an overview of cfDNA aneuploidy testing and present clinical cases where testing serendipitously detected cell free tumor DNA, resulting in an earlier diagnosis of a neoplastic process.

3:10 Liquid Biopsy Approaches For Detecting And Characterizing Human Cancer

Victor Velculescu, M.D., Ph.D., Professor of Oncology and Co-Director of Cancer Biology, Johns Hopkins Sidney Kimmel Cancer Center; Co-Founder, Personal Genome Diagnostics

Analyses of cancer genomes have revealed mechanisms underlying tumorigenesis and new avenues for therapeutic intervention. In this presentation, I will discuss lessons learned through the characterization of cancer genome landscapes, challenges in translating these analyses to the clinic, and new technologies that have emerged to analyze molecular alterations in the circulation of cancer patients as cell-free tumor DNA. These approaches have important implications for non-invasive detection and monitoring of human cancer, therapeutic stratification, and identification of mechanisms of resistance to targeted therapies..

3:40 The Hunt for Blood-Based Biomarkers for Diagnosis of Neurodegenerative Diseases

Robert M. Umek, Meso-Scale Diagnostics

While cerebrospinal fluid biomarkers and brain imaging have advanced our understanding of neurodegenerative diseases, there is considerable demand for blood-based biomarkers for diagnostics and use in clinical trials owing to the ease of sample acquisition and cost.  The status of the field as well as the challenges remaining will be considered.

3:55 Late Breaking Presentation

4:10 Mardi Gras Celebration in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall

6:00 Close of Day

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Wednesday, February 18

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

8:00 Plenary Session Panel 

9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


10:35 Chairperson’s Remarks

Michelle M. Hanna, Ph.D., CEO & Scientific Director, RiboMed

10:45 DNA Methylation as Cancer Biomarkers in Clinical Development

David Shames, Ph.D., Senior Scientist, Genentech

11:15 Development of DNA Methylation Markers for Early Lung Cancer Detection

Ite A. Laird-Offringa, Ph.D., Associate Professor,Surgery and of Biochemistry and Molecular Biology, Norris Cancer Center, Keck School of Medicine, University of Southern California

We are developing DNA methylation as a lung cancer marker. Cancer DNA is shed into the blood and can in principle be used to non-invasively detect a cancer signature in bodily fluids. We have mined our own and publicly available data to identify DNA methylation markers present with high penetrance in lung cancer tumors. Given that low-dose spiral computed tomography, the state-of-the-art and only tool currently available for lung cancer early detection, has a false positive rate of 96%, there is a great need for additional complementary biomarkers.

11:45 Quantitative and Sensitive Bisulfite-Free DNA Methylation Analysis from FFPE Tissues: Application to an 8-Gene Clinical Test for Brain Cancer Prognostics

Michelle M. Hanna, Ph.D., CEO & Scientific Director, RiboMed Biotechnologies, Inc.

Although the importance of epigenetic biomarkers such as DNA methylation has been recognized, the few clinical tests available are reported to have high failure rates with patient samples, even when examining a single gene. We have developed a sensitive, bisulfite-free method for quantitative analysis of DNA Methylation biomarker panels, even in compromised FFPE tissues. This allows DNA methylation biomarker panels discovered with bisulfite-based methods to be translated to the clinical laboratory, even when only small amounts of damaged DNA are available.

12:15 pm Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


1:40 Chairperson’s Remarks

Stuart S. Martin, Ph.D., Associate Professor, Physiology, Greenebaum Cancer Center, University of Maryland School of Medicine

1:50 Detection and Molecular Characterization of CTCs in Glioma Patients

Klaus Pantel, M.D., Professor & Chairman, Tumor Biology, University Medical Center Hamburg-Eppendorf

Glioblastoma multiform (GBM) is the most frequent and aggressive brain tumor in adults. The dogma that GBM spread is restricted to the brain was challenged by reports on extracranial metastases after organ transplantation from GBM donors. The CTC detection approach developed in this study is easily applicable as a companion diagnostic to identify patients with extracranial tumor cell spread, and it might be advisable to exclude these patients as organ donors.

2:20 Single Cell Genomic Analyses of Circulating Tumor Cells

Sunney Xie, Ph.D., Mallinckrodt Professor, Chemistry and Chemical Biology, Harvard University

We have demonstrated whole genome sequencing of circulating tumor cells (CTCs) with multiple annealing and looping-based amplification cycles (MALBAC). We discovered that CTCs of the same patient exhibit reproducible CNV gain and loss patterns, which are similar to the patterns of metastatic sites. Patients with the same cancer type have similar patterns while patients with different cancers have dissimilar patterns. The fact that CTC’s CNV patterns are tissue and cancer dependent offers prospects for noninvasive cancer diagnostics.

2:50 Targeting Microtentacles on Circulating Tumor Cells to Reduce Metastasis

Stuart S. Martin, Ph.D., Associate Professor, Physiology, Greenebaum Cancer Center, University of Maryland School of Medicine

Tumor cells generate dynamic membrane microtentacles (McTNs) in free-floating microenvironments, that promote the reattachment of circulating tumor cells in distant tissues. These McTNs arise from imbalances between microtubule extension and contraction of the actin cortex, and are detectable in freshly-isolated tumor cells from patients. By defining the cytoskeletal mechanisms underlying McTNs, we are clarifying how existing chemotherapies affect CTCs and identifying new therapeutic opportunities..

3:20 Late Breaking Presentation

3:50 Refreshment Break


4:00 Chairperson’s Remarks

Jae Lee, Ph.D., Chair and Senior Member, Biostatistics and Bioinformatics, Moffitt Cancer Center

4:10 Identifying and Overcoming Markers of Chemoresistance

Jason Baum, Ph.D., Associate Director, Companion Diagnostics, Research, Merrimack Pharmaceuticals

This talk will focus on the understanding of cancer cell survival networks to identify key biomarkers of resistance to chemotherapy. This includes initial proof-of-concept in a pre-clinical setting and translation into the clinic through the development of both tissue and blood-based diagnostic assays. Data from phase II clinical studies will illustrate the resistance of biomarker positive patients to chemotherapies across multiple indications, and the potential for targeted therapies to overcome this resistance.

4:40 The Impact of Tumor Heterogeneity on Clinical Biomarker Development using FFPE Tissue

Ken Chang, Ph.D., Senior Principal Scientist, Molecular Biomarkers and Diagnostics, Merck Clinical Labs

We have developed a “Concordance Calculator” to quantify reproducibility of multi-variant calls among Next Generation Sequencing replicates. This novel approach also allowed us to eliminate many different technical artifacts including Post Tissue Collection Modifications such as deamination and oxidation artifacts. Our most recent studies suggest that DNA mutation signatures as novel biomarkers for cancer diagnosis and prognosis are likely to be less sensitive to the impact of tumor heterogeneity than RNA-based expression signatures.

5:10 Prognostic Surrogate Markers for Survival, A Case Series for a Novel Antiangiogenic Therapy

M.A. Nezami, M.D., President, Cancer Epigenetics, Pacific Medical Center of Hope

Establishing the prognosis in majority of patients, especially with heterogeneous tumors, has been extremely challenging. One area of most recent attention in identifying surrogate markers for survival has been the vasculogenesis and its related serum markers. Here we present a series of cases treated with a novel antiangiogenic therapy and monitored through these markers to identify response that translated to prognosis and survival.

5:40 Close of Conference Program

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

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