This is an unprecedented time in biomolecular medicine. 1) Recent scientific findings have determined biofluids consist of circulating tumor cells (CTCs), cell-free nucleic acid (cfNA), or extracellular vesicles from multiple tissues within the body.
2) Rapid development of highly sensitive and accurate next-generation sequencing (NGS) technologies has allowed analysis of the role of these biomolecules, and has been rapidly adopted into molecular diagnostic laboratories. And 3) researchers are
empowered to analyze the role of these biomolecules in health, disease and treatment response leading to targeted therapies. However, there still remains insecurity associated with biofluid-based DNA/RNA analytical methods, which must be solved before
liquid biopsies can be implemented for broader routine applications. At The Liquid Biopsy Summit, experts present and consider process and technology refinements that can enable molecular liquid biopsies to become a fulcrum in the
future of precision medicine.
Wednesday, June 21
11:00 am Short Course Registration
11:30 am - 2:30 pm Pre-Conference Lunch Short Course*
SC1: Blood from Patient ‣ Needle ‣ Freezer ‣ Analysis ‣ Diagnosis: Biobanks and Their Critical Role in Moving Precision Medicine Forward
* Separate registration required.
2:00 Main Conference Registration
3:00 Organizer’s Opening Remarks
Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute
3:05 Chairperson’s Opening Remarks
Theral Timpson, Host and Producer, Mendelspod
3:15 FEATURED PRESENTATION: Pre-Analytical Variables in Blood Collection Impact on Precision Medicine
Carolyn Compton, M.D., Ph.D., Professor of Life Sciences, School of Life Sciences, Arizona State University;
Professor of Laboratory Medicine and Pathology, Department of Pathology, Mayo Clinic School of Medicine
This presentation focuses on the importance of evidence-based standardization of the pre-analytical steps in biospecimen acquisition and handling for liquid biopsies in order to assure reproducible, clinically meaningful analysis results. The work of
the Pre-analytics for Precision Medicine Project Team of the College of American Pathologists (CAP), the American Society of Clinical Oncology (ASCO)-CAP Liquid Biopsies Working Group and the Beau Biden Cancer Moonshot Blood Profiling Atlas in Cancer
(Blood PAC) will be highlighted.
3:45 CO-PRESENTATION: Improving the Quality of Circulating Tumor DNA Measurements by a Multi-Laboratory Assessment of Expert-Designed Reference Materials
Kenneth D. Cole, Ph.D., Group Leader, Bioassay Methods, National Institute of Standards and Technology
(NIST)
Russell K. Garlick, Ph.D., CSO, SeraCare Life Sciences, Inc.
Analytical validation of ctDNA assays must be accomplished before clinical validation. ctDNA assays present unique sensitivity and specificity challenges due to the biochemical nature of circulating cell-free DNA and multiple analytical measurement
techniques. This presentation discusses the design, development and characterization of expert-designed reference materials for use in a multi-lab assessment of ctDNA measurements. Commutability to patient samples and concordance between analytical
methods will be discussed.
4:30 Deep Sequencing QC: A Component Study of the FDA-Led Sequencing Quality Control Project Phase 2 (SEQC2)
Joshua Xu, Ph.D., Senior Computer Scientist, Division of Bioinformatics and Biostatistics, National Center for Toxicological
Research, Food and Drug Administration (FDA)
Deep sequencing focuses its sequencing reads on few small regions of the genome and thus achieves very sensitive detection of sub-clonal mutations. Liquid biopsy, an application of deep sequencing, has gained tremendous interest in the oncology research
community. Before deep sequencing is ready for use in clinical and regulatory settings, some major uncertainties need to be addressed. The FDA-led MicroArray Quality Control (MAQC) consortium seeks to assess validity and reliability, as well as
recommend sound analysis methods for deep sequencing and whole-genome sequencing in its fourth project that is also named Sequencing Quality Control Phase 2 (SEQC2).
5:00 PANEL DISCUSSION: Enhancing the Science and Clinical Utility of Liquid Biopsies
All agree that the potential of liquid biopsies will allow for detection of disease faster, diagnosis of disease earlier, and tracking of disease progression and treatment response more efficiently.
This panel discusses progress in:
- collection, preservation, and storage of biosamples
- advances in detection technologies
- determining reference materials and standards
- developing safe and effective blood profiling diagnostics
- creating an open database of liquid biopsy results
Moderator:
Theral Timpson, Host and Producer, Mendelspod
Panelists:
Kenneth D. Cole, Ph.D., Group Leader, Bioassay Methods, National Institute of Standards and Technology (NIST)
Carolyn Compton, M.D., Ph.D., Professor of Life Sciences, School of Life Sciences, Arizona State University; Professor of Laboratory Medicine and Pathology, Department of Pathology, Mayo Clinic School of Medicine
Russell K. Garlick, Ph.D., CSO, SeraCare Life Sciences, Inc.
Girish Putcha, M.D., Ph.D., Director of Laboratory Science, MolDx, Palmetto GBA
Joshua Xu, Ph.D., Senior Computer Scientist, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration (FDA)
5:30 Welcome Reception in the Exhibit Hall with Poster Viewing
6:30 Close of Day
Thursday, June 22
8:15 am Morning Coffee
8:45 Chairperson’s Remarks
Rebecca (Becky) Suttmann, MS, Senior Scientific Researcher, Oncology Biomarker Development, Genentech, Inc.
8:50 High-Content Analysis of Prostate Cancer Cells in Bone Marrow and Blood
James Hicks, Ph.D., Professor, Department of Biological Sciences, University of Southern California
It is rapidly becoming an article of faith that the ‘Liquid Biopsy,’ using a suite of cellular and molecular assays of blood or other body fluids, will become a key component in our progress toward precision medicine and personalized treatment
of cancer and other diseases. An array of blood-based assays is being developed that can provide a real-time window into the course of the disease and its response to treatment. HD-SCA is an integrated proteogenomic liquid biopsy platform for
assessing cancer heterogeneity at both the cellular and molecular levels. We will describe its integration into the Blood Profiling Atlas of Cancer (BloodPAC), a joint industry and academic effort spawned from the Biden Cancer Moonshot initiative
of 2016.
9:20 Retrospective Analysis of CellSearch CTC Enumeration Data across Clinical Trials
Rebecca (Becky) Suttmann, MS, Senior Scientific Researcher, Oncology Biomarker Development,
Genentech, Inc.
9:50 Multi-Component Liquid Biopsy Enabled by High-Throughput Optical Scanning Technologies
Zheng Ao, Ph.D., Postdoctoral Fellow, Biosciences Division, SRI International
Liquid biopsies provide a non-invasive means to access molecular and genetic information of the tumor. Using the high-throughput optical scanning technology here at SRI, we aim to interrogate not only the tumor cells in circulation (CTCs) but
also components of the tumor microenvironment such as cancer-associated fibroblasts (CAF), tumor-associated lymphocytes (TAL) and extracellular vesicles (EVs). This multi-component analysis is more representative of the whole tumor than CTCs
alone and will better enable us to put the puzzle together to understand the tumor through a tube of blood.
10:20 Coffee Break in the Exhibit Hall with Poster Viewing
11:00 Liquid Biopsy in Neurovascular Inflammation
J. Winny Yun, Graduate Assistant, JS Alexander Lab, Department of Molecular and Cellular Physiology, Louisiana
State University Health Sciences Center
Inflammatory cytokines promote cerebrovascular stress in several neurodegenerative diseases, including multiple sclerosis (MS), and may provoke endothelial disturbances, contributing to blood-brain barrier breakdown and exacerbation of disease.
We recently identified lymphatic endothelial-specific proteins in human brain tissue and in the serum, with altered expression in MS patient samples. This indicated the possibility that circulating lymphatic biomarkers may be derived from
brain endothelial cells in the form of circulating microparticles.
11:30 Detection of Human Cardiomyocyte Death Using Cell-Free DNA
Hai Zemmour, Research Scientist, Department of Developmental Biology and Cancer Research, The Institute
for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School
I present a totally new approach for studying onset cell type-specific death, especially cardiomyocyte degeneration in various pathological contexts, and envision a new type of blood test that aimed sensitive detection of tissue damage without
a priori suspicion of disease. I believe that such a tool will have broad utility in diagnostic medicine and in the study of human biology.
12:00 pm Circulating
RNA in the Blood of Cancer Patients: Isolation and Analysis to Determine Tumor Gene Expressions
Kathleen Danenberg, CEO, Liquid Genomics, Inc
Circulating tumor (ct) RNA contains the same mutational information as ctDNA but only for expressed genes and also allows quantitative determination of gene expression levels. CtRNA was successfully isolated from blood using Streck’s Cell-Free
RNA blood collection tube. Healthy individuals had uniformly low blood levels of ctRNA compared to cancer patients. Analysis of ctRNA in 329 NSCLC patients showed similar frequency of PD-L1 gene positivity (64%) as found by IHC of solid tissue
biopsies (66%).
12:30 Session Break
12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
2:15 Chairperson’s Remarks
Andries Zijlstra, Ph.D., Associate Professor, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center
2:20 Liquid Biopsies in Cancer Immunotherapy Clinical Drug Development
Shidong Jia, M.D., Ph.D., Founder & CEO, Predicine, Inc.
Cancer immunotherapy offers great promise where biomarkers have been shown to predict therapy outcome in various types of cancer patients. The talk describes the development and clinical application of a next-generation sequencing-based liquid
biopsy test to support cancer immunotherapy clinical trials.
2:50 Microfluidic Cell Tethering to Rapidly Measure Drug Responses in Patient Tumor Cells
Stuart S. Martin, Ph.D., Professor of Physiology, Greenebaum NCI Comprehensive Cancer Center,
University of Maryland School of Medicine
Non-adherent tumor cells display four phenotypes that are indicative of metastatic potential (microtentacles, clustering, deformability, stem cell sphere formation). However, technical challenges prevent high-resolution imaging of non-adherent
tumor cells. Integrating hydrophobic lipids into an engineered microfluidic surface tethers tumor cells while preserving the dynamic behaviors of non-adherent tumor cells. This technology enables rapid testing of patient cells for responses
to drug treatments that could influence CTC reattachment during metastasis.
3:20 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 FEATURED PRESENTATION: Epigenetic and Genetic Analysis of Circulating Biomarkers for Prostate Cancer Prognosis
Tim H-M Huang, Ph.D., Professor & Chair, Department of Molecular Medicine, University of Texas
Health Science Center at San Antonio
A continuous rise of serum PSA in patients after receiving radical prostatectomy is indicative of recurrent prostate cancer, or biochemical recurrence (BCR). Androgen-deprivation therapies appear effective for these patients when the BCR can
be detected earlier. The emergence of circulating biomarkers provides a new opportunity to non-invasively monitor disease recurrence and patients’ treatment responses. Shed into the bloodstream of cancer patients, these biomarkers
can be derived from cell-free DNAs (cfDNAs) and circulating tumor cells (CTCs). We have recently found that increased cfDNA methylation of androgen-biosynthesis loci is frequently associated with rising PSA in prostate cancer patients.
In a separate study, we have observed that increased cell rigidity, adhesiveness and deformability of CTCs represent novel biomarkers for BCR. These altered nanomechanical properties are often accompanied with the acquisition of an epithelial-mesenchymal
transition (EMT) phenotype in these circulating cells of advanced prostate cancer patients. Together, this integrative assay of exfoliated cell sources can improve detection of recurrent prostate cancer and is useful for monitor disease
progression.
4:30 Proteomic Alterations of Tumor Cell Adhesion Are Detectible in Patient Biofluids and Report on Their Outcome
Andries Zijlstra, Ph.D., Associate Professor, Department of Pathology, Microbiology
and Immunology, Vanderbilt University Medical Center
Proteins mechanistically involved in tumor cell migration and metastatic dissemination have the potential to serve as markers of invasive disease and predict patient outcome. The activity of the cell adhesion molecule ALCAM (Activated Leukocyte
Cell Adhesion Molecule) is regulated dynamically through proteolytic release of its extracellular domain. As such, the detection of shed ALCAM acts as a prognostic biomarker for solid tumors.
5:00 Heterogeneity of Cancer-Derived Extracellular Vesicles: The Emerging Role of Large Oncosomes
Dolores Di Vizio, M.D., Ph.D., Associate Professor, Pathology & Laboratory
Medicine, Biomedical Sciences, Cancer Biology Program, Cedars-Sinai Medical Center; Associate Professor, Medicine, University California, Los Angeles; Assistant Professor, Boston Children's Hospital, Harvard Medical School
Extracellular vesicles (EVs) are important mediators of intercellular mechanisms as they can shuttle from one cell to another a reservoir of functional molecules. EVs are being recognized as appealing biomarkers of diagnosis and prognosis.
We have demonstrated that the abundance of large oncosomes in the circulation and in tissues correlates with advanced disease in mouse models and human subjects, and that these vesicles are promising candidates for liquid biopsy approaches
through large-scale profiling of protein, DNA and mRNA.
5:30 Short Course Registration
5:45 - 8:45 Dinner Short Course*
SC2: Innovative Imaging Technologies for Patient CTCs
* Separate registration required.
Friday, June 23
7:30 am Breakfast Breakout Discussion Groups
Chew over breakfast and provocative discussion topics with your peers. These are moderated discussions with brainstorming and interactive problem-solving, allowing conference participants from diverse backgrounds to exchange ideas and
experiences and develop future collaborations around a focused topic.
Noncoding RNAs as Biomarkers in Liquid Biopsies
Moderator: Lynne Bemis, Ph.D., Chair, Biomedical Sciences, University of Minnesota
- What are the best samples, collection protocols and analyses used for RNA biomarkers currently?
- Are there some good clinically applicable examples of RNA biomarkers in use and in what diseases are they applied?
- What does the future look like for noncoding RNA biomarkers?
Liquid Biopsies in Cancer Immunotherapy Drug Development
Moderator: Shidong Jia, M.D., Ph.D., Founder & CEO, Predicine, Inc.
- Many liquid biopsy tests are available in the liquid biopsy space. How should one evaluate whether they are robust, reproducible and consistent across laboratories? In other words, what are the expected standards for analytical
validation of a liquid biopsy assay?
- ctDNA and CTC are the major focus in the current liquid biopsy space, and ctRNA technology is emerging. What are their strengths versus weaknesses?
- When a liquid biopsy test is done, how should the test report look in order to help clinicians understand the data and facilitate their day-to-day clinical decision-making?
Clinical Application of Circulating miRNA Biomarkers
Moderator: Lihan Zhou, Ph.D., CTO & Founder, MiRXES Pte Ltd.
- Brief update on latest trends in miRNA biomarkers
- Choice of technology for clinical application of circulating miRNA biomarkers
- Circulating miRNA vs. ctDNA and CTC, pros and cons for applications in disease screening, diagnosis, prognosis and response/recurrence monitoring
- Case studies on selected applications of circulating miRNA biomarkers
- Means of accelerating clinical adoption of circulating miRNA biomarkers
Circulating Nucleic Acid Biomarkers – Moving Beyond Oncology
Moderator: Jason Ross, Ph.D., Senior Research Scientist, Health and Biosecurity, CSIRO
- Most diagnostic tests use the principle of somatic mutation detection in cancer-derived ctDNA. How can we more broadly use these genetic variant detection technologies? Examples are organ transplant monitoring and fetal DNA detection
- What promise do DNA methylation cfDNA biomarkers offer outside of the oncology space? New developments demonstrate their utility as tissue integrity biomarkers
- Can circulating microRNAs be informative for applications such as infection or metabolic syndrome?
- Is it possible to use other properties of cfDNA, such as fragment size, for diagnostic tests outside of oncology?
Liquid Biopsies – What Marker Should I Use for Oncology?
Moderator: Steven A. Soper, Ph.D., Foundation Distinguished Professor, Department
of Chemistry, Department of Mechanical Engineering and Bioengineering; Director, Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas
- There are four major markers that comprise liquid biopsies – CTCs, cfDNA, proteins, and exosomes. What are the characteristics of these markers? Can they be used for managing all cancer stages?
- In terms of the isolation, what are the challenges?
- What information can be secured from each marker?
- What markers have FDA approval and for what indication?
- If at some point, liquid biopsy marker(s) can be used in early detection, which marker may be the most appropriate for screening?
9:00 Chairperson’s Remarks
Gary Spitzer, M.D., Director, Clinical Validity and Clinical Utility Evaluation, MolDX, Palmetto GBA
9:05 Clinical Utility Needs of ctDNA Assays versus Research Utility
Gary Spitzer, M.D., Director, Clinical Validity and Clinical Utility Evaluation, MolDX, Palmetto GBA
I present design of prospective transparent registries to validate the clinical utility of a test in a clear intent to study patient population. I also discuss obstacles of existing registry and trial design and present ideas on
how costs can be diminished through non-traditional data extraction techniques, but with emphasis on transparency, scientific independence and open data collection.
9:35 An Improved CTC Isolation Scheme for Pairing with Downstream Genomics: Demonstrating Clinical Utility in Metastatic Prostate, Lung and Pancreatic Cancer
Gayatri Premasekharan, Ph.D., Postdoctoral Fellow, Department of Urology & Division of Hematology Oncology, UCSF Helen Diller Cancer Research Center
10:05 Validating Liquid Biopsies in Cancer: How Sensitive Is Clinically Meaningful?
John Beeler, Ph.D., Vice President, Corporate and Business Development, Inivata, Inc.
10:20 Coffee Break in the Exhibit Hall with Poster Viewing
10:45 Colvera™: A ctDNA Liquid Biopsy Assay for Colorectal Cancer - Our Journey from Discovery to the Clinic
Jason Ross, Ph.D., Senior Research Scientist, Health and Biosecurity, CSIRO
We have developed Colvera™, a ctDNA liquid biopsy assay to diagnose and monitor colorectal cancer. The assay is based upon detecting circulating tumor DNA from two genes methylated in colorectal cancer, but unmethylated in
non-neoplastic tissue or blood. I discuss the journey we and our collaborators undertook: from biomarker discovery and validation, to assay design and then to clinical trials and the launch of a commercial lab test.
11:15 Development and Validation of a Pan-Cancer Liquid Biopsy Test: Criteria and Considerations
Honey V. Reddi, Ph.D., FACMG, Clinical Laboratory Director, The Jackson Laboratory
for Genomic Medicine
The presentation delineates the criteria that went in content evaluation, steps involved in validation including sample extraction methods, and also covers the limitations and challenges involved in the process.
11:45 Standardizing
the Circulating DNA Preanalytical Workflow in Translational Research
Phoebe Loh, Global Product Manager PreAnalytiX, Sample Technologies,
QIAGEN
Appropriate workflow set-up is necessary for effective transition of assays from research to clinical application. While introducing the PAXgene Blood ccfDNA System, this talk touches on considerations for creating a solid circulating
DNA preanalytical workflow which can be directly applied when moving to the next stage of translational research.
12:15 pm Session Break
12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:30 Chairperson’s Remarks
Lynne Bemis, Ph.D., Chair, Biomedical Sciences, University of Minnesota
1:35 KEYNOTE PRESENTATION: New Tools for Liquid Biopsies: Microfluidic Platforms for the Isolation of CTCs, cfDNA and Exosomes
Steven A. Soper, Ph.D., Foundation Distinguished Professor, Department of Chemistry,
Department of Mechanical Engineering and Bioengineering; Director, Center of BioModular Multi-Scale Systems for Precision Medicine, The University of Kansas
Liquid biopsies are generating great interest within the medical community due to the simplicity for securing important biomarkers to manage complex diseases, such as cancer-related diseases. These circulating markers consist of
CTCs, cfDNA and exosomes. We are developing a suite of microfluidic devices that can process whole blood directly and are engineered to efficiently search for a variety of disease-associated liquid biopsy markers from divergent
subpopulations comprising the tumor microenvironment.
2:20 Optofluidic Systems for On-Chip Detection of Cancer and Infectious Disease Biomarkers
Holger Schmidt, Ph.D., Professor, Electrical Engineering; Narinder Kapany
Chair of Optoelectronics; Director, W.M. Keck Center for Nanoscale Optofluidics, University of California, Santa Cruz
Optofluidic devices combine microfluidics with integrated optics, creating a single chip-based system for both preparation and analysis of biological samples such as liquid biopsies. I describe a versatile, optofluidic platform
using liquid-core optical waveguides for optical analysis of single biomolecules. Examples for its capabilities include amplification-free detection of Ebola RNA, multiplex detection of single influenza viruses and cancer DNA
biomarkers starting with a whole blood sample.
2:50 Multitarget Serum MicroRNA Assays for Early Detection of Lung and Gastric Cancers
Lihan Zhou, Ph.D., CTO & Founder, MiRXES Pte Ltd.
Lung and gastric cancers rank 1st and 3rd in mortality globally. Current screening methods of LDCT and gastroscopy are limited by specificity, invasiveness and cost. Using a proprietary ultra-sensitive qPCR technology, we have
developed serum miRNA assays to serve as an alternative for blood-based lung and gastric cancer screening. These assays have been validated in multi-center studies with encouraging accuracy in detecting Stage I and II cancers
(AUC>0.9).
3:20 Networking Refreshment Break
3:30 Sizing Up Cancer in Cell-Free DNA
Hunter R. Underhill, M.D., Ph.D., Assistant Professor, Pediatrics,
Division of Medical Genetics, University of Utah
Detection of cell-free DNA derived from non-metastatic solid tumors remains challenging. Identification of tumor-associated variants in cell-free DNA that occur at very low frequency (<1%) requires methods with ultra-high sensitivity.
Here, the role of size selecting for specific cell-free DNA fragment lengths to improve detection of solid tumors will be discussed. Size selection will be considered within the context of mutant allele enrichment and potential
effects on next-generation sequencing.
4:00 Making and Using RNA Standards: Can You Trust Your Genome-Scale Measurements?
Sarah A. Munro, Ph.D., Team Leader, Genome-Scale Measurements Group, Joint Initiative
for Metrology in Biology, National Institute of Standards and Technology (NIST)
When you’re assaying thousands of molecules at the same time, how do you know that you have the right answers? To make the 21st century of biology a reality, we need genome-scale measurement results we can trust. In our Joint
Initiative for Metrology in Biology (JIMB), we are working to systematically address these needs with RNA spike-in controls, mixture samples, and turn-key analysis tools.
4:30 tRNA Fragments in Accessible Samples: Expression, Biogenesis and Function
Lynne Bemis, Ph.D., Chair, Biomedical Sciences, University of Minnesota
tRNA fragments are common in RNA-seq libraries and were originally thought to be breakdown products. We identified a tRNA fragment that is present at high levels in the urine of patients with ovarian cancer and we have now
shown that its cleavage is regulated by the RNase, angiogenin. The function of this and other tRNA fragments in cancer cell lines will be described.
5:00 Close of Conference