The development of noninvasive methods to detect and monitor tumors continues to be a bottleneck in oncology research. Circulating cell-free DNA shows great promise, but still requires improvements and additional research before it becomes standard practice. At Cambridge Healthtech Institute’s 6th Annual Circulating Cell-Free DNA symposium, leading clinicians and researchers from academia and industry will come together to address advances as well as existing challenges in this rapidly growing field. This year’s event will place emphasis on early detection, therapeutic monitoring and drug response, and making cfDNA standard clinical practice.

Final Agenda

Thursday, March 14

7:00 am Registration Open and Morning Coffee (Continental Foyer)

IMPROVING SENSITIVITY AND EARLY DETECTION
Continental 4

8:25 Chairperson’s Opening Remarks

Abhijit Patel, MD, PhD, Associate Professor, Yale University School of Medicine


8:30 KEYNOTE PRESENTATION: Triple-D PCR and Mutation Enrichment Technologies for the Analysis of Clinically Relevant DNA Alterations in Liquid Biopsies

G-Mike-MakrigiorgosG. Mike Makrigiorgos, PhD, Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School

With the increasing interest in treatment assessment using liquid biopsy and circulating DNA, sensitive and multiplexed detection of tumor-derived alterations in blood is desirable. We provide novel forms of digital PCR (“triple-d PCR”), as well as mutation enrichment-based methods that (a) enable several orders of magnitude improvement of detecting mutations or microsatellite instability than currently possible; (b) are highly multiplex-able; (c) reduce cost of analysis. Application in circulating DNA from clinical cancer samples will be presented.

9:00 Clinical Applications of Droplet Digital PCR for Liquid Biopsies

Dobrovic_AlexAlexander Dobrovic, PhD, Group Leader, Translational Genomics and Epigenomics, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.

Droplet digital PCR (ddPCR) has proven capable of meeting many of the challenges in assessing ctDNA. A particular advantage of ddPCR is a rapid turnaround time with results being potentially available in less than six hours after receipt of a blood sample. A second advantage is absolute quantification of templates which facilitates monitoring. However, the identification of a tumour-specific change is a necessity. Driver mutations are ideal but chromosome rearrangements and DNA methylation changes are potential alternatives.

9:30 Ultra-Sensitive Mutational Analysis in Cell-Free DNA by Digital PCR and NGS Technologies

Tam_RachelRachel Tam, PhD, Senior Scientific Researcher, Genentech

Circulating cell-free DNA (cfDNA) in plasma offers a non-invasive approach to monitor tumor molecular profiling in real-time at multiple time-points, detection of emerging genomic alterations associated with drug resistance and clarifying cancer prognosis and diagnosis of cancer recurrence or progression. We developed an ultra-sensitive droplet digital PCR (ddPCR) approach and molecular-tagged NGS technologies to detect actionable cancer biomarkers in cfDNA.

Sera-Care 10:00 Building and Implementing Liquid Biopsy Assays with Industry’s Most Patient-Like Reference Standards

Clement_OmoOmo Clement, PhD, Senior Product Marketing Manager, Clinical Genomics

To ensure their clinical utility, NGS-based liquid biopsy assays must achieve exquisite sensitivity. We will discuss how sustainable, patient-like, highly-multiplexed ctDNA standards help laboratories and NGS assay developers save time while achieving and validating sensitivity to as low as AF0.1%.

10:30 Coffee Break in the Exhibit Hall with Poster Viewing

IMPROVING SENSITIVITY AND EARLY DETECTION (CONT.)
Continental 4

11:15 FEATURED PRESENTATION: Multi-Analyte Assays for the Detection and Monitoring of Cancers

Chetan BettegowdaChetan Bettegowda, MD, PhD, Assistant Professor, Neurosurgery and Oncology, Johns Hopkins University School of Medicine

We describe a blood test that can detect eight common cancer types through assessment of the levels of circulating proteins and mutations in cell-free DNA. We applied this test, called CancerSEEK, to 1005 patients with nonmetastatic, clinically detected cancers of the ovary, liver, stomach, pancreas, esophagus, colorectum, lung, or breast. CancerSEEK tests were positive in a median of 70% of the eight cancer types. The sensitivities ranged from 69 to 98% for the detection of five cancer types for which there are no screening tests available for average risk individuals.

11:45 Ultrasensitive Detection of Cancer Using cfDNA Methylation Sequencing

Zhou_XianghongXianghong Jasmine Zhou, PhD, Professor, Pathology and Laboratory Medicine, UCLA

We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios.

12:15 pm Combining Immunophenotyping and Artificial Intelligence for Early Cancer Detection

Kumar_Amit_CFDXAmit Kumar, PhD, President, CEO, Anixa Diagnostics

Flow-cytometry is used to analyze leukocytes to identify tumor-bearing patients from a simple blood draw. A neural network is used to distinguish between healthy donors and biopsy verified cancer patients. Sensitivity and specificity are exceptional.

12:30 Session Break

BioRad 12:40 Luncheon Presentation: Checking your Answers: Monitoring Response to Immunotherapy via plasma ctDNA

Neumann_Karlin_GeorgeGeorge Karlin-Neumann, PhD, Director, Scientific Affairs, Digital Biology Center, Bio-Rad Laboratories, Inc

Due to the complexities of the immune system, it is unlikely that pre-treatment predictors of immunotherapy outcomes in cancer patients will be highly accurate.  An important complementary method providing early outcomes prediction is emerging via plasma monitoring of ctDNA levels.

1:15 Session Break

MONITORING RESIDUAL DISEASE AND THERAPEUTIC RESPONSE
Continental 4

1:55 Chairperson’s Remarks

Mike MakrigiorgosG. Mike Makrigiorgos, PhD, Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School


2:00 Ultrasensitive Measurement of ctDNA for Therapy Monitoring and Early Detection

Patel_AbhijitAbhijit Patel, Associate Professor, Department of Therapeutic Radiology, Yale University

Our group has developed NGS-based methods that use molecular and computational error suppression techniques to enable ultrasensitive detection of ctDNA without prior knowledge of a tumor’s mutation profile. This presentation will describe our work in the areas of therapeutic response assessment and early cancer detection.


2:30 Utility of Different Forms of cFNA in Cancer Detection and Progression

Hoon_DavidDavid S. B. Hoon, PhD, MSc, Chief of Scientific Intelligence; Director, Molecular Oncology; Director, JWCI Sequencing Center, John Wayne Cancer Institute

cFNA assessed for monitoring cancer progression and response to treatment has shown to be increasingly promising as an informative blood biopsy. However, the major forms of cFNA that have been assessed are selective gene mutations. This approach limits the utility of monitoring in specific cancer patients when these mutations have low frequency. Assessment of other forms of different cFNA and multimarker approaches can improve monitoring tumor progression.

3:00 A Sensitive, Mid-Plex ctDNA Detection Method to Identify Mechanisms of Drug Resistance

Shell_ScottScott Shell, PhD, Global Oncology Lead, Scientific Affairs, Agena Bioscience

MassARRAY-based liquid biopsy applications are mid-plex panels that deliver results in under two days.  This presentation will review the performance of these applications on well characterized commercial reference materials, and cfDNA from NSCLC patients, with comparisons to qPCR and ddPCR.

3:30 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall

4:15 Analysis of ctDNA for Personalized Response Assessment and Surveillance

Diehn_MaximilianMaximilian Diehn, MD, PhD, 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. In this presentation I will describe application of the high throughput sequencing-based Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) method to detection of ctDNA molecular residual disease following curative-intent therapy in early stage lung cancer.

4:45 Treatment Monitoring and Residual Disease Detection using Personalized Circulating Tumor DNA Analysis

Bradon McDonald, Murtaza Lab, Translational Genomics Research Institute

Accurate treatment monitoring can guide individualized management of cancer patients, but current diagnostic approaches lack adequate sensitivity. We have developed TARDIS to simultaneously analyze multiple patient-specific cancer mutations from plasma DNA. We observed 93.5% sensitivity in control samples (mutation fraction: 1%-0.03%) from only 5-8ng of DNA, and find a strong association between ctDNA detection and disease presence in clinical samples from early stage patients. TARDIS shows promise as a useful tool for enabling non-invasive monitoring of tumor dynamics.

5:15 EFIRM Liquid Biopsy for Early Cancer Detection and Therapeutic Monitoring

Wong_DavidDavid Wong, DMD, DMSc, Associate Dean of Research and Felix & Mildred Yip Endowed Distinguished Professor

EFIRM-Liquid Biopsy (eLB) provides the most accurate targeted detection that can assist clinical treatment decisions for non-small cell lung cancer (NSCLC) where tyrosine kinase inhibitors (TKI) that can extend the disease progress free survival period of these patients. eLB requires only 40 µl of sample volume and no sample processing. Reaction time is fifteen minutes and can be performed at the point-of-care or high throughput reference lab using plasma or saliva. eLB detects actionable EGFR mutations in NSCLC patients with >95% concordance with biopsy-based genotyping.

5:45 Reception in the Exhibit Hall with Poster Viewing

6:45 Close of Day

Friday, March 15

8:00 am Registration Open and Morning Coffee (Continental Foyer)

MONITORING RESIDUAL DISEASE AND THERAPEUTIC RESPONSE (CONT.)
Continental 4

8:55 Chairperson’s Remarks

Filip Janku, MD, PhD, Associate Professor, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center

9:00 Liquid Biopsies as a Tool for Assessment of Therapeutic Efficacy, Tumor Burden and Pharmacodynamics

Janku_FilipFilip Janku, MD, PhD, Associate Professor, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center

Molecular testing of liquid biopsies using the circulating tumor cell-free DNA offers minimally invasive approaches for molecular diagnostics in cancer, which can be used to guide cancer treatment. Early data suggest that the circulating tumor cell-free DNA can correlate with tumor burden and its dynamic changes can reflect therapeutic outcomes. Also, dynamic monitoring of the circulating tumor cell-free DNA can be used as a pharmacodynamics marker for development of targeted therapies.

9:30 Monitoring Cancer through the Blood

Paweletz_CloudCloud Paweletz, PhD, Head, Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute

Noninvasive assessment of tumor genotype using cell free DNA (cfDNA) represents an emerging technology that can overcome many of the current challenges in personalizing NSCLC care. There are a variety of assays available, some focused and rapid and others broad but more cumbersome (e.g. NGS). Indeed, some of these cfDNA genotyping technologies are being offered commercially for clinical use; however, appropriate clinical application is uncertain and clinical validation efforts have been inconsistent. Here we present our institutional experiences implementing liquid biopsies into NSCLC care.

10:00 Early Response Monitoring with Circulating Tumor DNA in Lung Cancer

Husain_HatimHatim Husain, MD, Assistant Professor of Medicine, Division of Medical Oncology, Department of Medicine at UC San Diego

Non-invasive drug response biomarkers for early assessment of tumor response can enable adaptive therapeutic decision-making for individualized patient treatment and proof-of-concept for target inhibition of tumor cells by investigational drugs. Findings suggest that tyrosine kinase inhibitors induced tumor apoptosis within days of initial patient dosing. We demonstrate that early monitoring of ctDNA by non-invasive sampling provides temporal and quantitative dissection of early tumor response.

10:30 Coffee Break in the Exhibit Hall with Poster Viewing

MONITORING RESIDUAL DISEASE AND THERAPEUTIC RESPONSE (CONT.)
Continental 4

11:15 NEW SPEAKER: Blood-Based Tumor Mutational Burden as a Predictor of Clinical Benefit in Non-Small-Cell Lung Cancer Patients Treated with Atezolizumab

Todd Riehl, PhD, Associate Group Clinical Science Director, Product Development Oncology, Genentech

Here, we describe a novel, technically robust, blood-based assay to measure TMB in plasma (bTMB) that is distinct from tissue-based approaches. Using a retrospective analysis of two large randomized trials as test and validation studies, we show that bTMB reproducibly identifies patients who derive clinically significant improvements in progression-free survival from atezolizumab (an anti-PD-L1) in second-line and higher NSCLC. Collectively, our data show that high bTMB is a clinically actionable biomarker for atezolizumab in NSCLC.

11:45 Precision Digital PCR Monitoring of Circulating Tumor DNA Indicates Longitudinal Therapeutic Response in Metastatic Cancer

Wood-Bouwens_ChristinaChristina Wood-Bouwens, Lab Manager, Ji Research Group, Cellular and Molecular Biology, Stanford University

Single-color digital droplet PCR enables absolute quantification of mutation-bearing cell-free molecules for a fraction of the cost of next generation sequencing. Our novel assay has a molecular limit of detection down to three mutation ctDNA molecules, and can be used with non-amplified template. I will describe how this technology will be used to create customized mutation assays for individual cancer patients on a high-throughput scale, enabling rapid longitudinal monitoring of ctDNA.

12:15 pm An Intravascular Magnetic Wire for the High-Throughput Retrieval of Circulating Tumor Cells in vivo

Vermesh_OphirOphir Vermesh, PhD, Postdoctoral Fellow, Multimodality Molecular Imaging Lab (MMIL), Stanford University

Current methods for the isolation of circulating tumour cells (CTCs) or nucleic acids present in a standard clinical sample of only 5–10 ml of blood provide inadequate yields for early cancer detection and comprehensive molecular profiling. Here, we report the development of a flexible magnetic wire that can retrieve rare biomarkers from the subject’s blood in vivo at a much higher yield.

12:45 Close of Symposium

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