Molecular traces of cancer can be found in circulation early in the disease. Analysis of biomarker signatures are yielding remarkable insights into early detection, disease progression, therapy monitoring and treatment selection in oncology. Liquid biopsy offers the promise to achieve greater success in our treatment of cancer, but many aspects of this field need to be improved in the isolation and characterization of circulating tumor cells, cell-free circulating DNA, exosomes and extracellular vesicles. This meeting will shed light on novel emerging technologies, analytical validation and clinical implementation. Don’t miss the industry’s leading event on liquid biopsy learn about important discoveries and network with your peers.
Scientific Advisory Board
Stefanie Jeffrey, M.D., John and Marva Warnock Professor, Surgery; Chief, Surgical Oncology Research, Stanford University School of Medicine
Stuart S. Martin, Ph.D., Associate Professor, Physiology, Greenebaum NCI Cancer Center, University of Maryland School of Medicine
Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University, Medical Center Hamburg-Eppendorf
Steven A. Soper, Ph.D., Professor, Micro and Nanofabricated Tools for Biological Discovery and Medical Diagnostics, University of Kansas
Monday, February 20
10:30 am Conference Program Registration Open
11:50 Chairperson’s Opening Remarks
Stefanie Jeffrey, M.D., John and Marva Warnock Professor, Surgery; Chief, Surgical Oncology Research, Stanford University School of Medicine
12:00 pm Smart Tumors, CTCs and Liquid Biopsies
George W. Sledge, M.D., Professor, Medicine; Chief, Division of Oncology, Stanford University School of Medicine
Cancers kill because they are resistant to currently available therapies. The promise of CTC and ctDNA technologies is that they will allow either earlier diagnosis of small tumors, or provide crucial evidence regarding drug resistance at a point where that resistance is reversible. What are the prospects for CTC and ctDNA technologies reversing potentially lethal drug resistance, and how will we employ them in the clinic?
12:30 Isolation and Molecular Characterization of Breast Cancer Stem Cells
Max S. Wicha, M.D., Madeline and Sidney Forbes Professor, Oncology; Founding Director Emeritus, University of Michigan Comprehensive Cancer Center
There is substantial evidence that tumors are driven by a subpopulation of cells that display stem cell properties and that these cells mediate tumor metastasis and contribute to treatment resistance. A number of agents designed to target these cancer stem cells are now in early stage clinical trials. The development of robust platforms to isolate and molecularly characterize circulating tumor cells at single cell resolution should greatly facilitate these studies.
1:00 Session Break
1:10 Luncheon Presentation I: CTC Enrichment by Parsortix™- Clinical Applications
Robert Zeillinger, Ph.D., Associate Professor, Molecular Oncology Group, Medical University of Vienna
1:40 Luncheon Presentation II: Transformational Techniques and Clinical Utilities for Blood Based Biopsies Using CellSieve™ Microfilters
Cha-Mei Tang, Sc.D., President & CEO, Creatv MicroTech Inc
Daniel Adams, Senior Research Scientist, Creatv MicroTech Inc
CellSieve™ filters capture CTCs and stromal cells from the blood of cancer patients. We describe their prevalence and profiles in the context of early detection and cancer pathogenesis, redefining our understanding of CTCs, stromal cells and blood based diagnostics.
2:10 Session Break
2:30 Chairperson’s Remarks
Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology, University, Medical Center Hamburg-Eppendorf
2:40 Tumor-Educated Platelets as a Blood-Based Liquid Biopsy Platform for Cancer Diagnostics
Myron G. Best, Ph.D. Student, Neurosurgery, Cancer Center Amsterdam, VU University Medical Center Amsterdam, The Netherlands
Blood-based ‘liquid biopsies’ provide a means for minimally invasive molecular diagnostics. Confrontation of blood platelets with tumor cells via transfer of tumor-associated biomolecules (tumor-educated platelets; TEPs) is an emerging concept. We performed RNA-sequencing of >1000 platelet samples covering multiple tumor types. Our results indicate that platelets provide a valuable platform for cancer diagnostics. The unprecedented ability of TEPs to pinpoint the location of the primary tumor advances the use of liquid biopsies for cancer diagnostics.
3:10 Unveiling the Circulating Tumor Endothelial Cell Cluster
Min-Han Tan, Ph.D., Principal Investigator, Biodevices and Diagnostics, Institute of Bioengineering and Nanotechnology
Circulating cell clusters have been reported for decades in cancer patients as malignant entities with a key role metastasis. Contrary to this consensus, we describe a discrete population of tumor-derived circulating cell clusters with similar cytomorphology and EMT marker expression, but with origins traced instead to the tumor endothelia.
3:40 About Chomsky, DNA Patterns, Non-Coding RNAs and Cancer Patients
George A. Calin, M.D., Ph.D., Professor, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center
The newly discovered differential expression in numerous tissues, key cellular processes and multiple diseases for several families of long and short non-codingRNAs (ncRNAs, RNAs that do not codify for proteins but for RNAs with regulatory functions), including the already famous class of microRNAs (miRNAs) strongly suggest that the scientific and medical communities have significantly underestimated the spectrum of ncRNAs whose altered expression has significant consequences in diseases.
4:10 Recovery & State-of-the-Art Molecular Analysis of Single (Pure) CTCs using DEPArray Based Technology
Farideh Bischoff, Ph.D., Chief Clinical Development Officer, North America Menarini Silicon Biosystems
DEPArray™ Platform delivers precision in the preparation circulating tumor cells for MDx. Complete workflows have been developed for the recovery of pure single CTCs that are amenable to downstream NGS approaches, including targeted panel and low pass copy number analysis.
4:40 Refreshment Break and Transition to Plenary Session
5:00 Plenary Keynote Session
6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing
7:30 Close of Day
Tuesday, February 21
7:30 am Registration Open and Morning Coffee
8:00 Plenary Keynote Session
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, Surgery; Chief, Surgical Oncology Research, Stanford University School of Medicine
10:15 Single-Cell Phenotypic Analysis of Circulating Tumor Cells
Dino Di Carlo, Ph.D., Professor, Bioengineering, California NanoSystems Institute; Director, Cancer Nanotechnology Program, Jonsson Comprehensive Cancer Center, University of California, Los Angeles
We have developed several workflows for integrating Vortex trapping technology with downstream phenotypic analysis of single circulating tumor cells (CTCs). I will present our results in analyzing single-cell secretions from CTCs in an automated microfluidic workflow and proof of concept clinical studies to evaluate expression levels programmed death ligand 1 (PD-L1) on Vortex-isolated CTCs from non-small cell lung cancer patients on checkpoint inhibitor therapy.
10:45 Circulating Tumor DNA Analysis – Clinical Impact
John Strickler, M.D., Assistant Professor, Medicine, Duke University Medical Center
Interest in ctDNA to diagnose, monitor, and profile solid tumors has surged. The increased use of ctDNA reflects a desire to minimize procedural risk to the patient, while applying therapies tailored to a patient’s specific tumor profile. Already, ctDNA is routinely used to guide therapeutic decision-making, and to identify patients for clinical trials. In this presentation, the opportunities and challenges of utilizing ctDNA in the clinic will be discussed.
11:15 Microfluidics for the Efficient Selection of Disease-Associated Extracellular Vesicles from Plasma
Steven A. Soper, Ph.D., Foundation Distinguished Professor, Department of Chemistry, Department of Mechanical Engineering; Director, Center of BioModular Multi-Scale System for Precision Medicine, The University of Kansas
Liquid biopsies are generating interest within the biomedical community due to the simplicity for securing important markers. These circulating markers consist of CTCs, cell free DNA and extracellular vesicles. We are developing a microfluidic that can process plasma and efficiently search for disease-associated extracellular vesicles comprising divergent subpopulations. These subpopulations emanate from different cancer cell types and can supply complimentary clinical information.
11:45 A Novel, High Yield, High Complexity, and Scalable Active-Extraction of Circulating Cell-Free DNA (ccfDNA) from Stabilized Plasma
Hamid Khoja, Ph.D., Principal Scientist, Research & Development, Covaris Inc.
In this talk we present data illustrating the effectiveness of the Covaris Adaptive Focused Acoustics™ (AFA) enabled truXTRAC ccfDNA active extraction method. Specifically designed for dissociating and extracting ccfDNA from histone-ccfDNA and other protein-ccfDNA covalently-linked complexes which occur in BCT®-stabilized plasma, the magnetic bead based truXTRAC ccfDNA enables scalable and automatable high throughput sample processing. Furthermore, DNA sequencing confirmed that truXTRAC ccfDNA processed samples resulted in higher library complexity, mapped reads, coverage uniformity, and variant detection sensitivity when compared to passive ccfDNA extraction methods.
12:00 pm VTX-1 Liquid Biopsy System: The Next Step in CTC Isolation
Steve Crouse, M.S., MBA, Chief Commercial Officer, Vortex Biosciences, Inc.
The VTX-1 Liquid Biopsy System isolates and collects intact CTCs directly from whole blood in as little as 1 hour. Clinical data will demonstrate how the proprietary approach results in the capturing of more clinically relevant CTCs with >60% CTC recovery and best in class CTC purity.
12:15 Session Break
12:25 Luncheon Presentation I: Highly Sensitive Isolation and Molecular Characterization of CTC for Early Detection of Tumor Invasion
Patrizia Paterlini-Brechot, M.D., Ph.D., Professor, Faculty of Medicine, University Paris Descartes
ISET allows to isolate fixed and live tumor cells with sensitivity down to one per 10 mL of blood. We show NGS analyses of single cells enriched by ISET® and of tumor cells before and after isolation and culture.
12:55 Luncheon Presentation II: Improving NGS-Based Liquid Biopsy Mutation Detection with Anchored Multiplex PCR
Josh Stahl, MSc, MBA, CSO, General Manager, ArcherDX
Liquid biopsies have the potential to be a less invasive method than traditional biopsies to detect advanced solid tumor mutational status. Anchored Multiplex PCR (AMP™) is target enrichment chemistry for NGS that is uniquely suited for highly fragmented material such as liquid biopsy-derived ctDNA. AMP-based ctDNA library preparation uses molecular barcoded adapters to remove PCR duplicates, correcting for both PCR and sequencer-derived sequencing errors while enabling accurate allele frequency quantitation.
1:25 Refreshment Break in the Exhibit Hall with Poster Viewing
2:00 Chairperson’s Remarks
Steven A. Soper, Ph.D., Foundation Distinguished Professor, Department of Chemistry, Department of Mechanical Engineering; Director, Center of BioModular Multi-Scale System for Precision Medicine, The University of Kansas
2:10 Comparison of Different CTC Isolation Technologies in the Context of Clinical Utility
Pamela Paris, Ph.D., Professor, Urology, University of California, San Francisco
This presentation will provide an overview of some of the CTC platforms available today. The strengths and limitations of the CTC platforms will be discussed based on first-hand use in the laboratory. Examples will be provided for each platform’s potential clinical utility.
2:40 Integrated Extracellular Vesicle Profiling for Minimally Invasive Diagnosis and Early Detection of Cancer
Andrew K. Godwin, Ph.D., Chancellors Distinguished Chair, Biomedical Sciences and Endowed Professor, Professor and Director of Molecular Oncology, Pathology and Laboratory Medicine; Deputy Director, The University of Kansas Cancer Center; Director, Biospecimen Shared Resource Kansas Bioscience Authority; Eminent Scholar, University of Kansas Medical Center
Extracellular vesicle (EV), primarily nano-sized vesicles of endocytic origin referred to as exosomes, are produced and released by most cells types under normal physiologic and in diseased states. Considered little more than garbage cans whose job was to discard unwanted cellular components, recent discoveries have sparked interest as circulating biomarkers. Ways to exploit these circulating EVs and their payloads of proteins and nucleic acids using miniaturized biomedical assays will be discussed.
3:10 Orthogonal Endpoints in Prostate Cancer Circulating Tumor Cell Biomarkers
Joshua M. Lang, M.D., MS, Assistant Professor, Medicine, Carbone Cancer Center, University of Wisconsin
Prostate cancer is a heterogeneous disease with complex, intersecting mechanisms of resistance to targeted therapies. Prospective clinical trials interrogating CTC biomarkers across protein, gene expression and genomic endpoints identify acquired resistance mechanisms and pharmacodynamic biomarkers.
3:40 3D Telomere Signatures Indicate Prostate Cancer Progression in CTC’s Isolated with ScreenCell Technology
Sabine Mai, Ph.D., Professor, University of Manitoba, Director, The Genomic Centre for Cancer research and Diagnosis, Manitoba Institute of Cell Biology/RIOH, University of Manitoba
Using 3D Telomere Technology and circulating tumor cells isolated using the ScreenCell device, we examined intermediate risk prostate cancer patients prior to their radical prostatectomy. 3D nuclear telomeric profiles correctly identified patients with stable vs. progressive disease prior to RP.
4:10 Hollywood Oscar Dessert Reception in the Exhibit Hall with Poster Viewing
5:00 Breakout Discussions in the Exhibit Hall
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. Pre-registration to sign up for one of the topics will occur a week or two prior to the Event via the App.
The Use of RNA Biomarkers for Blood-Based Cancer Diagnostics
Myron G. Best, Ph.D. Student, Neurosurgery, Cancer Center Amsterdam, VU University Medical Center Amsterdam, The Netherlands
- Available biosources and biomolecules for blood-based RNA biomarkers
- Techniques/approaches to measure RNA in these biosources
- Most potential applications and approaches for blood-based RNA biomarkers
- Combined cfDNA/cfRNA tests for cancer diagnostics
Cell-Free DNA Profiling In The Clinic
Dana W. Y. Tsui, Ph.D., Assistant Attending Geneticist; Member, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center
- Applications for molecular profiling in oncology
- Applications for monitoring treatment efficacy (e.g. transplantation)
- Practical considerations (Sample processing, logistics and quality controls)
6:00 Close of Day
Wednesday, February 22
7:00 am Registration Open
7:00 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee
8:00 Plenary Keynote Session
10:00 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall
10:50 Chairperson’s Remarks
Klaus Pantel, M.D., Professor and Founding Director, Institute of Tumor Biology,
University, Medical Center Hamburg-Eppendorf
11:00 TP53 Mutations for Early Cancer Detection: Challenges Revealed by Duplex Sequencing
Rosana Risques, Ph.D., Assistant Professor, Pathology, University of Washington
The detection of tumor-specific mutations in clinically accessible samples could enable early cancer detection, but it is limited by the high error rate of DNA sequencing. Duplex Sequencing reduces errors by scoring mutations only present in both strands of DNA. Our studies in ovarian cancer demonstrate that TP53 Duplex-Sequencing detects cancer cells with high sensitivity. However, they also reveal prevalent TP53 mutations in non-cancerous tissue, which challenges clinical applications.
11:30 Clonal Hematopoiesis of Indeterminate Potential (CHIP): Common Pre-Malignant State for Blood Cancers
Siddhartha Jaiswal, M.D., Ph.D., Research Fellow and Staff Pathologist, Massachusetts General Hospital and Harvard University; Broad Institute, MIT
We recently identified that clonal hematopoiesis is a common finding in the elderly, with over 10% of individuals over the age of 70 harboring such a mutated clone in their blood. The presence of this condition raises the subsequent risk of developing hematologic malignancy by ~10-fold, making this a bona fide pre-malignant state. Early diagnosis of this condition opens the future possibility of preventing blood cancer in a high-risk population.
12:00 pm Liquid Biopsies and the Early Diagnosis of Cancer
Luis A. Diaz, M.D., Head, Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center
12:30 Session Break
12:40 Luncheon Presentation: Analytical and Clinical Validation of Cell-free DNA Assays in Oncology: Efficient Translation to Clinical Care
Minetta Liu, M.D., Associate Professor, Department of Oncology, Department of Laboratory Medicine and Pathology, Mayo Clinic
Tumor specific molecular alterations increasingly play a part in drug selection and prognosis in cancer. Technologies that allow for the detection of specific mutations in cell free DNA (cfDNA) isolated from the peripheral blood have led to the concept of “liquid biopsies”. This has immediate applications in colorectal cancer with potential utility in solid tumor malignancies. This session will discuss efforts to validate molecular biomarkers and develop solutions to promote rapid translation into clinical practice.
1:10 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing
1:50 Chairperson’s Remarks
Stuart S. Martin, Ph.D., Associate Professor, Physiology, Greenebaum NCI Cancer Center, University of Maryland School of Medicine
2:00 Circulating Tumor DNA Analysis for Personalized Cancer Detection and Monitoring
Maximilian Diehn, M.D., Ph.D., Assistant Professor, Radiation Oncology, Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University
Circulating tumor DNA (ctDNA) represents a promising biomarker for sensitive, specific, and dynamic detection of disease burden in cancer patients. Mutations in tumor-derived DNA represent ideal potential biomarkers since they are highly specific to tumor cells and involved in disease pathogenesis. However, even in advanced cancer patients concentrations of ctDNA are often low and difficult to detect. We have developed a novel, ultra-sensitive and specific method for detection of circulating tumor DNA called Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq). This method was developed specifically for detection of ctDNA in non-small cell lung cancer patients, although it is broadly applicable to other cancer types. In this presentation I will describe our recent work on applications of ctDNA analysis in a variety of clinical settings.
2:30 Circulating Tumor Cell Clusters as Precursors of Breast Cancer Metastasis
Nicola Aceto, Ph.D., Assistant Professor, Oncology, Department of Biomedicine, University of Basel
Using mouse models with color-coded primary tumors, we determine that CTC-clusters are oligoclonal units with up to 50-fold increased metastatic potential compared to single CTCs. In patients with breast and prostate cancer, the presence of CTC-clusters correlates with disease progression. With RNA sequencing followed by loss of function studies, we identify plakoglobin as a major mediator of CTC-clustering and metastasis. Thus, we find that CTC-clusters are a highly efficient, yet targetable mechanism of cancer dissemination.
3:00 Substantial Interindividual and Limited Intraindividual Genomic Diversity among Tumors from Men with Metastatic Prostate Cancer
Peter S. Nelson, M.D., Professor, Medicine, Division of Oncology, Fred Hutchinson Cancer Research Center
The success of precision oncology is dependent on identifying different therapeutic vulnerabilities in tumors between different individuals but the consistent presence of the vulnerability in all or most tumors or tumor cells within an individual patient. In this presentation I will describe the molecular assessments of metastatic prostate cancers and circulating tumor DNA (ctDNA) to assess inter- and intra-individual tumor diversity with implications for treatment selection.
3:30 Session Break
3:40 Chairperson’s Remarks
Stuart S. Martin, Ph.D., Associate Professor, Physiology, Greenebaum NCI Cancer Center, University of Maryland School of Medicine
3:45 Scalable Approach for Whole-Exome Sequencing of Cell-Free DNA from Patients with Metastatic Cancer
Viktor Adalsteinsson, Ph.D., Group Leader, Broad Institute of MIT and Harvard
Whole-exome sequencing of cell-free DNA (cfDNA) may enable comprehensive profiling of tumors from blood. Here, we describe a scalable approach to qualify and sequence whole-exomes of cfDNA. Whole-exome sequencing of cfDNA and biopsies from 23 patients revealed high concordance of clonal somatic mutations (90%), copy number alterations (80%), mutational signatures, and neoantigens. Screening of 879 blood samples from 333 metastatic cancer patients revealed 42% with sufficient tumor content for whole-exome sequencing.
4:15 Simultaneous Detection of Living Circulating Tumor Cells and Cancer Related Extracellular Vesicles in Blood by a Molecular Beacon Based Biochip
L. James Lee, Ph.D., Professor, Chemical and Biomolecular Engineering, The Ohio State University
A novel and facile immune-lipoplex nanoparticle (ILN) biochip is developed to simultaneously capture and characterize living circulating tumor cells (CTCs) and cancer related extracellular vesicles (EVs) in patient blood. Antibodies are used to capture CTCs and EVs in a microfluidic device, while molecular beacons encapsulated in cationic lipoplex nanoparticles and fluorescence labelled antibodies are used to detect coding and non-coding RNA targets and membrane protein targets respectively in both CTCs and EVs. The identified CTCs are alive for further interrogation such as drug resistance.
4:45 A Clinically Feasible Strategy to Concurrently Profile Prostate Cancer in Circulation and Bone using High-Definition Single Cell Analysis
Amado Zurita-Saveedra, M.D., Associate Professor, MD Anderson
5:15 Close of Conference Program
Stay on for these Tri-Conference Symposium, taking place at February 23-24, 2017 at Moscone South Convention Center
Circulating Cell-Free DNA