2015 Next Generation Dx Summit

2015 Predictive Cancer Biomarkers Track Banner

Cancer biomarkers have become an essential component of patient care. With discovery efforts ongoing, the next phase towards translation will involve validation and demonstration of clinical utility. Cambridge Healthtech Institute's Eighth Annual Predictive Cancer Biomarkers will focus on the steps needed to manage the new treatment paradigm from treating clinical symptoms to targeting genomic pathways. Focus will be given to the use of circulating tumor material to follow patients peripherally, both with known metastatic disease and post-surgery. Throughout the event, top cancer researchers will present their latest discoveries, case studies, and best practices to decrease late-stage diagnosis and improve patient outcomes.


SC8: Detection and Characterization of Circulating Biomarkers 

*Separate registration required,

Day 1 | Day 2 | Short Courses | Download Brochure 


7:30 am Main Conference Registration & Morning Coffee


8:30 Chairperson’s Opening Remarks

Jennifer Morrissette, Ph.D., Scientific Director, Clinical Cytogenetics Laboratory; Clinical Director, Center for Personalized Diagnostics (CPD), University of Pennsylvania Perelman School of Medicine

8:40 Phylomics®: From Omics to Precision Medicine

Amri HakimaHakima Amri, Ph.D., Associate Professor; Vice President, Phylomics LLC ; Co-Director, Physiology and CAM Graduate Programs, Department of Biochemistry and Cellular and Molecular Biology, Georgetown University School of Medicine

The multiple levels of heterogeneity evident within and among populations, both healthy and diseased, complicate the mining and interpretation of biological big data. In cancer, which is an evolutionary disease, heterogeneity has hampered the search for validated biomarkers for early disease detection, and it has complicated the task of finding the disease-driving clonal aberrations. Therefore, evolution-compatible methods of analysis, such as phylogenetics, have a potentially useful role in cancer studies, prognosis and diagnosis. In this talk, we present a paradigm shift, whereby the evolutionary meaning of the data is brought out and applied to produce natural class determination, predictive biomarker recognition, and modeling of the evolutionary processes of disease development from the population to the individual patient, hence personalized medicine. Phylomics® is a non-invasive and cost-effective diagnostic tool. 

9:10 Ranking Omics Data to Discover Biomarkers

Corrado PriamiCorrado Priami, Ph.D., President & CEO, The Microsoft Research and University of Trento Centre for Computational and Systems Biology

An approach based on ranking of measurements is presented to identify patient signatures. The signature can be used to define biomarkers with respect to diseases, stratification of patients with respect to interventions or even toxicology of drugs with respect to doses and number of deliveries. I will present the approach and I’ll show examples of its application.

9:40 The Usefulness of Genomics in Clinical Medicine: Mutation Detection by NGS for Clinical Trials and Patient Stratification

Jennifer MorrissetteJennifer Morrissette, Ph.D., Scientific Director, Clinical Cytogenetics Laboratory; Clinical Director, Center for Personalized Diagnostics (CPD), University of Pennsylvania Perelman School of Medicine

Genomic testing in the routine care for a variety of malignancies reliably detects somatic mutations and can provide insight into disease development, prognosis and therapeutic options. This talk will focus on our approach to mutation detection in malignancies, including capture of difficult to sequence regions of hematological malignancies (e.g. large FLT3-ITDs), and mutation detection of actionable mutations in glioblastoma multiform (e.g. EGFRvIII). An overview of clinical impact of testing and case studies where our NGS panels have influenced treatment will be discussed.  


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


10:55 Chairperson’s Remarks

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

11:00 Circulating MicroRNAs and Other Nucleic Acids in Treatment Monitoring

Anton WellsteinAnton Wellstein, M.D., Ph.D., Professor, Oncology, Georgetown University

This talk will describe the methodology of microRNA analysis from the circulation and application to treatment monitoring. Potential pathway specific findings will also be discussed.


11:30 Detection and Analysis of DNA/RNA Biomarkers from Hematological Cancer, Solid Tumors and TBI Patient Samples

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

Fluorescent detection of ccf-DNA/RNA biomarkers from CLL, solid tumor and TBI patient blood and plasma samples (20-100ul) is achieved in 10-15 minutes using an AC dielectrophoretic (DEP) microarray. For CLL, PCR and sequencing results are comparable to “gold standard” procedures. Fragment size analysis is being carried to determine apoptotic and necrotic origins of CLL and solid tumor ccf-DNA, which may ultimately have important diagnostic value.

Janssen12:00 pm NGS of Circulating Tumor Cells from the CELLSEARCH® System

Charles Saginario, Ph.D., Scientist, CRS Labs, Janssen Diagnostics


12:30 Epigenetic Profiling of DNA Methylation to Categorize Breast Tumor Aggressiveness

Adam MarshAdam Marsh, Ph.D., Associate Professor, Bioinformatics and Computational Biology, University of Delaware

Women with triple-negative genotypes for the 3 common marker mutations for breast cancer are still at significant risk for this disease. We identify a suite of differentially methylated CpG sites between Normal and Tumor breast tissues that indicate a high degree of epigenetic conservation among different triple-negative patients who have developed aggressive breast tumors. Subtle epigenetic shifts in methylation status may provide a key line of evidence for assessing tumor risk and deciding between surgery or therapy.

NuGen1:00 Luncheon Presentation: Targeted NGS Analyses of Clinical Samples for SNPs, CNVs, Gene Fusions and More

Joe Don HeathJoe Don Heath, Ph.D., Vice President, Market Development Diagnostics, NuGEN

A novel approach for custom targeted sequencing of both DNA and RNA will be described. Sensitive variant detection in genomic DNA derived from fresh and FFPE tissues will be demonstrated as well as utilization of the enrichment technology as a rapid, cost-effective tool for the discovery of novel gene fusions and the detection of known, clinically-relevant gene fusions using a 500+ cancer gene screening panel.

1:30 Refreshment Break in the Exhibit Hall with Poster Viewing


2:00 Chairperson’s Remarks

Louis Fiore, M.D., Executive Director, MAVERIC, Boston VA Healthcare System

2:05 The Department of Veterans Affairs Precision Oncology Program

Louis FioreLouis Fiore, M.D., Executive Director, MAVERIC, Boston VA Healthcare System

The VA Precision Oncology Program systematically genotypes cancer patients and enrolls them into a cohort so that they can be matched to biomarker-driven clinical trials. This talk presents a collaborative model for integration of research and clinical care. The program addresses important issues such as bringing clinical trials to patients, identification of cases across a network of hospitals, sharing of clinical data with research partners and collection of patient-centered and patient-reported outcomes.

2:35 NGS for Patient Screening and Treatment Selection for NCI’s MPACT and Match Trials

P. Mickey WilliamsP. Mickey Williams, Ph.D., Director, Molecular Characterization Laboratory (MoCha), Frederick National Laboratory for Cancer Research


3:05 Predictive Biomarkers for Targeted Cancer Therapy

Baolin Zhang, Ph.D., Senior Investigator, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration

The ability to identify the subsets of patients with molecularly defined cancers could significantly improve patient outcome. This presentation will discuss the major challenges in the discovery, qualification and regulatory review of predictive cancer biomarkers. Emphasis will be placed on the recent efforts of the US Food and Drug Administration in facilitating the joint development of therapeutic products and in vitro companion diagnostic devices (IVDs) that are essential for the safe and effective use of the corresponding therapeutic products.

KMC-ESA3:35 Automated Multimodal, High-Multiplex, Quantitative Molecular Platform Solution for Complicated Companion Diagnostics 

Lily KongLilly Kong, Senior Director, Assay Development, Qiagen

Clinicians across multiple disciplines are asking complex questions for tailored therapies. Automated multimodal, high-multiplex, quantitative PCR is the ideal next generation of MDx. Modaplex provides precise, robust and simple solutions to meet the needs of next generation cancer diagnostics and therapeutic modalities. We will discuss how our “All in One Tube” technology makes it possible to develop unique, highly multiplexed, multimodal, quantitative and qualitative IVDs to interrogate dozens of biomarkers in one tube. Using this, drug developers can capture the full value of their therapies.

Cellecta3:50 Driver-Map™ Panels: Quantitative, Multiplex PCR, Target Enrichment Based NGS for Drug Target Discovery

FrangouGus Frangou, Ph.D., Director, Clinical Diagnostics, Cellecta Inc.

Driver-Map™ Biomarker Discovery Panels offer a novel high-throughput PCR based sequence enrichment platform to comprehensively assess the genomic landscape for both solid tumors and hematologic malignancies from archived FFPE, blood and bone marrow aspirate samples. Specifically, Driver-Map analyzes common genomic "hot spot" regions that are frequently mutated in 250 genes related to cancer treatment, prognosis and diagnosis. In addition, simultaneous quantitative target gene expression analysis using competitive multiplex-PCR amplicons for ~3000 genes and computational network modeling, facilitates the rapid identification of cancer driver genes or gene models, pathway analysis to identify commonalities across tumor type(s), and supporting pharmacogenetic information. The talk will provide insight into how this functional genomics pipeline can be used to expediently identify novel biomarkers and therapeutic targets for cancer en masse.

4:05 Refreshment Break in the Exhibit Hall with Poster Viewing



Moderator: Robert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories 

Panelists: Avni B. Santani, Ph.D., Assistant Professor, Clinical Pathology, University of Pennsylvania School of Medicine; Scientific Director, Molecular Genetics Laboratory, The Children’s Hospital of Philadelphia

Helen Fernandes, Ph.D., Director, Molecular Pathology, Pathology & Laboratory Medicine, Weill Cornell Medical College

  • Selecting genes for new panels
  • Informatics and analysis
  • Building clinical infrastructure ensure action on mutations

5:50 Wine & Cheese Pairing Welcome Reception in the Exhibit Hall with Poster Viewing

6:50 Close of Day

Day 1 | Day 2 | Short Courses | Download Brochure 


7:15 am Registration

7:30 – 8:25 Problem-Solving Breakout Discussions with Continental Breakfast

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.

Matching Patients to Biomarker-Driven Clinical Trials

Moderator: Louis Fiore, M.D., Executive Director, MAVERIC, Boston VA Healthcare System

Practical issues related to embedding discovery and clinical validation of cancer biomarkers in the clinical care ecosystem. This discussion will take a deeper dive into issues raised at the previous days presentation by Dr. Fiore "The Department of Veterans Affairs Precision Oncology Program".

  • Technical and regulatory challenges in the use of data from Electronic Healthcare Records
  • Cultural and ethical issues of embedding research activities in clinical care
  • Matching patients to clinical trials - bringing trials to patients

Circulating Biomarkers as Liquid Biopsies

Moderator: Anton Wellstein, M.D., Ph.D., Professor, Oncology, Pharmacology and Medicine, Georgetown University Medical School; Associate Director, Basic Science, Lombardi Comprehensive Cancer Center

  • Potential information content of tissue vs liquid biopsies
  • Complementary use of tissue and liquid biopsies
  • False signals in tissue vs liquid biopsies
  • Sequential use of tissue versus liquid biopsies     

Topic to be Announced

Moderator: Russell Garlick, Ph.D., CSO, SeraCare Life Sciences

  • Introduction to SeraCare Life Sciences
  • Importance of a flexible quality control system for NGS testing
  • Brief overview of Seraseq biosynthetic mutation mix technology


8:25 Chairperson’s Opening Remarks

Robert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories

8:30 Utility of Implementing Clinical NGS Assays as Standard of Care in Oncology

Helen FernandesHelen Fernandes, Ph.D., Director, Molecular Pathology, Pathology & Laboratory Medicine, Weill Cornell Medical College

The presentation will address the practical processes that need to be adopted for a NGS-based assay to be run in a routine clinical laboratory. The topics will address specific challenges encountered from the preanalytical to the analytical and postanalytical phases of the process. Details on achieving libraries with optimal quality from various types of specimens will be discussed. Factors that affect the implementation of the analytical process and the variability encountered in the interpretation of variants will be highlighted. Strategies for recognizing and dealing with the barriers will be included.

9:00 Development and Implementation of Clinical NGS Testing: Assay Development and Informatic Challenges

Robert DaberRobert D. Daber, Ph.D., Director, Research and Development and Sequencing Operations, Bio-Reference Laboratories

As genomic technologies continue to advance and new bio-markers emerge, rapid NGS assay development becomes critical in the age of Precision Diagnostics. Here we will discuss emerging methods to capture important biological markers and their associated informatic challenges during both the development and implementation phases.

9:30 Implementation of Clinical Exome Sequencing

Avni SantaniAvni B. Santani, Ph.D., Assistant Professor, Clinical Pathology, University of Pennsylvania School of Medicine; Scientific Director, Molecular Genetics Laboratory, The Children’s Hospital of Philadelphia

With the advent of next generation sequencing (NGS), diagnostic laboratories are faced with unprecedented challenges in incorporating this technology in the clinical setting. This presentation will provide a comprehensive overview on the key considerations for implementation of clinical exome sequencing including resource allocation, assay development, compliance, bioinformatics, data management, analysis and interpretation of data.  

SeraCare10:00 Qualitative and Quantitative Tools for Performance Monitoring in of NGS Tumor Profiling Assays

Russell Garlick, Ph.D., CSO, SeraCare Life Sciences

Biosynthetic mutation mixes for NGS assays are a powerful way to monitor the daily run performance--tracking both qualitative and quantitative measures. Unlike cell lines, biosynthetic mutation mixes offer a means to cover wide varieties of mutations and the ability to ‘tune’ them to specific allelic frequencies to evaluate the assay sensitivity and specificity. An overview of their development and use in a clinical setting will be discussed.

10:15 Sponsored Presentation (Opportunity Available)

10:30 Coffee Break in Exhibit Hall with Poster Viewing

PLENARY KEYNOTE SESSION: Click here for details 

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

1:50 Chairperson’s Opening Remarks

2:00 KEYNOTE PRESENTATION: Monitoring the Cancer Genome in Plasma Using Circulating Tumor DNA

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

Circulating cell-free tumor DNA (ctDNA) can be used to probe cancer genome dynamics via plasma samples. When a biopsy is unavailable, ctDNA can be used as a ‘liquid biopsy’ to assess sensitivity and resistance to targeted therapies. Quantification of ctDNA is informative for cancer prognosis, response or relapse. If cancer progresses, cancer evolution can be studied noninvasively by genome-wide analysis of ctDNA in plasma.

3:00 Close of Predictive Cancer Biomarkers

Day 1 | Day 2 | Short Courses | Download Brochure 

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