Clinical sequencing is enabling personalized medicine to combat a host of diseases, from cancers to infections. This program will discuss applications of circulating tumor cells, liquid biopsy utilization, and the technologies and approaches to strategize and optimize processes to bring developments to the clinic and beyond. The Clinical NGS Diagnostics program will feature a lineup of experts ranging from academia to industry to government, coming together to share not only their advancements, but opportunities for growth and improvement as they deliver the next generation of sequencing technology to the cases that need it the most.

Final Agenda

Arrive Early for:

SUNDAY, MARCH 10, 2:00 - 5:00 PM (AFTERNOON SHORT COURSES)

SC3: NGS Assay Selection, Validation and Compliance - Detailed Agenda

SUNDAY, MARCH 10, 5:30 - 8:30 PM (DINNER SHORT COURSES)

SC12: Clinical Informatics: Returning Results from Big Data - Detailed Agenda

MONDAY, MARCH 11, 8:00 - 11:00 AM (MORNING SHORT COURSES)

SC17: Next-Generation Sequencing as a Diagnostics Platform - Detailed Agenda

Monday, March 11

10:30 am Conference Program Registration Open (South Lobby)

MULTIPLEX PLATFORMS AND MICROFLUIDICS TECHNOLOGIES
103

11:50 Chairperson’s Opening Remarks

L. James Lee, PhD, Helen C. Kurtz Professor, Department of Chemical and Biomolecular Engineering, the Ohio State University


12:00 pm KEYNOTE PRESENTATION: A PDX/Organoid Biobank of Advanced Prostate Cancer for Disease Modeling and Therapeutic Screening

Kelly_KathleenKathleen Kelly, PhD, Lab Chief, Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute

Organoid cultures provide a technology to culture epithelial cancers that otherwise do not propagate in vitro. We have established a preclinical platform of PDX- and patient biopsy-derived metastatic castrate resistant prostate cancer (mCRPC) organoids that is experimentally facile for high throughput and mechanistic analysis. The genetic and phenotypic variability and stability of models, genetic manipulations, and the utility of such a platform for drug sensitivity determination will be discussed.

12:30 Extracellular Vesicular RNAs for Cancer Diagnosis and Therapy

Lee_JamesL. James Lee, PhD, Helen C. Kurtz Professor, Department of Chemical and Biomolecular Engineering, the Ohio State University

We have developed facile biochip technologies to detect target microRNAs and mRNAs in individual extracellular vesicles (EVs) using advanced molecular beacons designs and nanoparticles. These biochip technologies have been successfully applied to detect and manipulate EV RNAs for cancer diagnosis in liquid biopsy and potentially for cancer therapy.

 

1:00 Enjoy Lunch on Your Own

NUCLEIC ACID ANALYSIS IN EXTRACELLULAR VESICLES AND CTCs
8

2:30 Chairperson’s Remarks

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

2:40 The Whole Transcriptional Landscape of Circulating Tumors Cells in Metastatic Breast Cancer

Lang_Julie Julie E. Lang, MD, Associate Professor of Clinical Surgery; Director, Breast Cancer Program, Department of Surgery, Keck School of Medicine, University of Southern California

The aim of our study was to evaluate if RNA Seq of circulating tumor cells could serve as a surrogate for biopses of macrometastases. We evaluated treatment opportunities based on circulating tumor cell profiles and tracked them under the selection pressure of systemic therapy in Stage IV breast cancer. RNA Seq of circulating tumor cells may be used to discover molecular alterations that are potentially clinically actionable.

3:10 Large Oncosomes as a Source of Cancer-Specific Circulating Biomarkers

DiVizio_Dolores Dolores Di Vizio, MD, PhD, Division of Cancer Biology and Therapeutics, Departments of Surgery, Biomedical Sciences and Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center

Extracellular vesicles (EVs) are heterogeneous membrane enclosed structures harboring molecular cargo from the cell of origin. Large oncosomes are a novel subtype of EV that is released by highly migratory cancer cells. Large oncosomes contain abundant tumor-derived cargo, which can be analyzed upon purification from plasma and other biological fluids. Here we show analyses of protein, RNA and DNA in controlled system and patient plasma.

3:40 Molecular Analysis of Circulating Tumor Cells, Extracellular Vesicles and Nucleic Acids as Liquid Biopsy in the Follow-Up of Metastatic Breast Cancer Patients to Stratify Patients for Targeted Therapy

Kasimir-Bauer_Sabine Prof. Dr. Sabine Kasimir-Bauer, Head of Research Laboratory, Department of Gynecology and Obstetrics, University Hospital Essen

The so-called liquid biopsy is discussed to be a surrogate marker for therapy stratification of metastatic breast cancer patients. We compared and analyzed RNA profiles enclosed in circulating tumor cells or extracellular vesicles and performed mutational analysis of cell-free DNA (cfDNA) in plasma samples (Next Generation Sequencing) in the follow-up of the disease to get insights into their feasibility for therapy stratification and to predict therapeutic options.

RareCyte 4:10 An Open, End to End, and Flexible Platform for Scalable CTC Collection, Identification, and Analysis

George_TadTad George, PhD, Senior Director of Platform, Applications, RareCyte

RareCyte provides instrumentation and consumables that enable an exquisitely sensitive, accurate, simple, and repeatable workflow from liquid biopsy to single cell isolation. The open and end to end RareCyte CTC workflow will be the focus of this talk.

4:40 Refreshment Break and Transition to Plenary Session


5:00 Plenary Keynote Session   (Room Location: 3 & 7)

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

7:30 Close of Day

Tuesday, March 12

7:30 am Registration Open and Morning Coffee (South Lobby)


8:00 Plenary Keynote Session   (Room Location: 3 & 7)

9:15 Refreshment Break in the Exhibit Hall with Poster Viewing

UNLEASHING THE POWER OF NGS
101 & 102

10:15 Chairperson’s Remarks

Phil Febbo, MD, CMO, Senior Vice President, Clinical Genomics, Illumina

10:25 The Path to Clinical Whole Genome Analysis as Standard of Care

Febbo_PhillipPhil Febbo, MD, CMO, Senior Vice President, Clinical Genomics, Illumina

Clinical whole genomes are feasible and affordable and will become the standard of care when there is utility to having a definitive and comprehensive genomic assessment. With continued application and publication of results, health care providers will become more informed about the feasibility and utility of clinical whole genome sequencing; with improved sample-to-answer sequencing technologies, more laboratories will be able to perform whole genomes; and, through significant collaborative and industry efforts, there will be more robust annotation, interpretation, and actionability of the genome. When these initial barriers are overcome, use will increase, the benefit to patients assessed, and adoption will occur in those settings where patient outcomes improve.

10:55 Translating Human Genetic Insights into Drug Discovery Impact

Janna Hutz, PhD, Senior Director, Head of Data Sciences & Scientific Infrastructure, Eisai

It is well established that therapeutic targets supported by robust genetic association data are more likely to result in approved medicines than therapeutic targets that are not. There is now a growing appreciation of how insights from human genetics can go beyond target discovery and validation, to impact across the spectrum of drug discovery and development. We have unprecedented substrate and opportunity to realize a new paradigm in human genetics guided discovery and development of precision therapeutics.

11:25 AI Genomics: Changing the Cancer Landscape

Riley Ennis, COO, Freenome

Traditional cancer screening test development has yielded major gaps in performance and patient outcomes. This is due, in part, to the limitations of analyzing a small, fixed number of genes or proteins, limiting the inputs necessary to evolve and compensate for false positive results. Come hear how AI genomic approaches are being leveraged to create smart, blood-based diagnostic tests that improve in performance over time with each sample processed.

Millipore-Sigma-green11:55 Faster Together: Avoid Development Roadblocks by Partnering Early with MilliporeSigma

Bagga_SavitaSavita Bagga, PhD, MBA, Invitro Diagnostics Segment, Marketing Manager, MilliporeSigma

Explore how we connect researchers with MilliporeSigma experts to exchange challenges/perspectives on IVD development.  With more understanding of customer pain points, our R&D teams can offer customized solutions for the IVD industry's specific needs and accelerate the path to commercialization.


12:25 pm Session Break

InterpaceDiagnostics 12:35 Luncheon Presentation: Seeking Coverage and Reimbursement for New Technologies

Greg Richard, Chief Commercial Officer, Interpace Diagnostics

Securing coverage and reimbursement for new technologies is a difficult and arduous process for providers.  While payers have adopted favorable coverage policies for some molecular diagnostics, strategies such as requiring pre-authorization and delegating decision-making for laboratory services to third parties make the process more complex and less transparent. However, there are some tactics that can potentially be useful in overcoming these challenges; this talk will review these options and provide examples of their success.

1:05 Session Break

1:35 Refreshment Break in the Exhibit Hall with Poster Viewing

OPTIMIZATION OF LABORATORY WORKLOAD FOR NGS
103

2:05 Chairperson’s Remarks

Jennifer J.D. Morrissette, PhD, FACMG, Scientific Director, Clinical Cancer Cytogenetics; Clinical Director, Center for Personalized Diagnostics, Department of Pathology, University of Pennsylvania

2:10 NCI Resources to Support Biospecimen-Based Research

Moore_HelenHelen M. Moore, PhD, Branch Chief, Biorepositories and Biospecimen Research Branch, NCI

The U.S. National Cancer Institute offers evidence-based best practice documents, an online literature and SOPs database, and research programs to support the collection of high quality research biospecimens. These resources will be discussed as well as new biobanking programs being developed under the Cancer Moonshot initiative.

2:40 A Moving Target: Optimization and Evolution of NGS Testing in Myeloid Malignancies

Morrissette_JenniferJennifer J.D. Morrissette, PhD, FACMG, Scientific Director, Clinical Cancer Cytogenetics; Clinical Director, Center for Personalized Diagnostics, Department of Pathology, University of Pennsylvania

This talk will discuss how our laboratory incorporated longitudinal testing for our hematological malignancy patients, based on data demonstrating the shift of clones containing variants that respond to targeted therapies, including FLT3, IDH1 and IDH2. The extremely poor outcome for patients harboring a TP53 mutation and the gene variants known to respond to targeted therapies has highlighted the need to rapidly identify variants. The final section will discuss the validation of a rapid NGS test in the laboratory.

3:10 A Multi-Institutional Collaborative Approach to Reducing Costs and Driving Standardization of Oncology NGS

Segal_JeremyJeremy Segal, MD, PhD, Assistant Professor; Director, Genomic and Molecular Pathology, University of Chicago

Next-generation sequencing (NGS) oncology diagnostics are continuing to grow in complexity and represent a substantial developmental and validation challenge for clinical laboratories. Academic laboratories are mainly working independently, creating a variety of different assays on various chemistry platforms with variable gene lists, bioinformatics algorithms and reported features. This assay variability raises questions of cross-site concordance and puts academic labs at a regulatory disadvantage. To lower NGS-associated laboratory costs and begin to work towards cross-site assay standardization, we assembled a collection of 17 academic laboratories to pursue a novel type of large-scale hybrid capture reagent purchase capable of supporting standardization efforts while permitting flexible design for site-specific gene content. This talk will address the formation of the Genomic Oncology Academic Laboratory (GOAL) consortium, the details of the group purchase including design specifications and performance, and future directions related to assay and bioinformatics standardization.

3:40 Tissue Print Technologies for Biopsy-Based  Molecular Biomarker Studies

Sandra M. Gaston  PhD, Director, Molecular Biomarkers Analytic Laboratory, Radiation Oncology, University of Miami Miller School of Medicine

Many tissue biomarker tests are designed to use FFPE specimens as a source of RNA and/or DNA, but the allocation of FFPE tissue for pathology and research is becoming increasingly challenging, particularly for biopsy specimens. Tissue prints provide a practical alternative for obtaining RNA, DNA and protein biomarkers for molecular analyses without compromising the specimen for diagnostic H&E and immunohistochemistry.  With biopsies, tissue prints support molecular biomarker studies of valuable specimens that may otherwise be significantly limited or entirely unavailable for research. Because tissue prints are snap frozen rather than fixed in formalin, the purified tissue print RNA and DNA is  of  high quality and suitable for advanced biomarker analysis. We will review applications of tissue print techniques to biopsy-based studies of RNA, DNA and protein biomarkers, to molecular biomarker mapping and to biorepository specimen annotation.

4:10 St. Patrick’s Day Celebration in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall

6:00 Close of Day

Wednesday, March 13

7:30 am Registration Open and Morning Coffee (South Lobby)

8:00 Plenary Keynote Session   (Room Location: 3 & 7)

10:00 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall

HIGH-THROUGHPUT SCREENING AND MODELS FOR PERSONALIZED MEDICINE
1 & 2

10:50 Chairperson’s Remarks

David B. Roth, MD, PhD, Director, Penn Center for Precision Medicine; Chair, Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania

11:00 Precision Oncology in AML: Choosing the Right Drugs to Treat

Cherry_SaraSara Cherry, PhD, Professor of Microbiology, Scientific Director, High-throughput Screening Core; Director, Program for Chemogenomic Discovery, University of Pennsylvania

Acute myeloid leukemia (AML) is the most common form of adult acute leukemia, with ~16,000 new cases per year in the US and 10,000 deaths. Despite intensive treatment regimens the 5-year survival is ~35%. New targeted therapies have shown promise, but are not curative, and only available to subsets of patients. We developed a new pipeline to directly screen patient tumor cells for sensitivity to 3000 clinically actionable drugs and are currently developing this into a diagnostic for personalized therapies in AML.

11:30 Personalized Cancer Models for Target Development and Precision Oncology

Kemp_Chris_PRXChristopher Kemp, PhD, Full Member, Human Biology, Fred Hutchinson Cancer Research Center

A major goal of precision oncology is to utilize genomic information to inform patient care. While there are spectacular examples of success, for the great majority of cancer patients, genomic information is insufficient to guide patient care or select effective therapeutic options. We have developed an approach that employs high-throughput functional testing with both siRNA and drugs using patient tumor cell cultures. This functional data combined with genomic analysis is used to distinguish driver from passenger mutations and identify novel drug targets and potentially effective drugs specific to a given patient.

12:00 pm Functional Approaches to Define Tumor Intrinsic and Extrinsic Targets for Personalized Therapeutic Regimens

Tyner_JeffJeffrey Wallace Tyner, PhD, Associate Professor, Developmental & Cancer Biology, Oregon Health & Science University (OHSU) Knight Cancer Institute

To overcome these obstacles in delivery of precision medicine based on genomic-only approaches, my research program has developed a pipeline of functional tools for analysis of primary cells from patients with hematologic malignancies. This pipeline is comprised of siRNA, CRISPR/Cas, and small-molecule libraries to interrogate the genes and signaling pathways required for cancer cell growth. Simultaneous application of these functional approaches with genomic data has accelerated our understanding of pathways that contribute to neoplasia. In addition, these assays are completed in a clinically relevant time frame of three days, such that the data from these assays can be used to directly inform therapeutic strategies, even in the absence of genomic information.

12:30 Enjoy Lunch on Your Own

1:10 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing

MACHINE LEARNING TO MAKE BIG DATA CLINICALLY ACTIONABLE
153

1:50 Chairperson’s Remarks

Matthew Lebo, PhD, FACMG, Director, Bioinformatics, Partners Personalized Medicine; Instructor, Pathology, Brigham and Women’s and Harvard Medical School

2:00 Machine Learning for Data Driven Decision Making of Clinical Trials

Hua_KevinKevin Hua, PhD, Senior Manager, AI Machine Learning Development, Digital Health Intelligence Group, Bayer

Clinical trials are expensive business expenditures. Advances in AI/machine learning and data mining technology and availability of data make data-driven decision making possible in drug development. We would like to present a case study where wearable devices and deep learning models are used to help clinical scientists make faster and more accurate decisions during clinical trials.

2:30 Informatics Approaches to Reducing the Sanger Burden in Clinical NGS Laboratories

Lebo_mattMatthew Lebo, PhD, FACMG, Director, Bioinformatics, Partners Personalized Medicine; Instructor, Pathology, Brigham and Women’s and Harvard Medical School

Recent work has highlighted the accuracy and completeness of NGS such that these additional assays may not be required, especially in the realm of orthogonal confirmation of variants. However, many of these studies have been underpowered to accurately define thresholds for ensuring high confidence in NGS variant calling. In this talk, we’ll discuss algorithmic and machine learning approaches to tackle this problem, demonstrating the ability to dramatically reduce, but crucially not eliminate, the burden of orthogonal confirmation in germline NGS assays.

3:00 From Pixels to Phenotypes: Analysis Of Cellular Images With Multi-Scale Convolutional Neural Networks

godinez_WilliamWilliam J. Godinez, PhD, Research Investigator, Novartis Institutes for BioMedical Research (NIBR)

Large-scale cellular imaging and phenotyping is a widely adopted strategy for understanding biological systems and chemical perturbations. Quantitative analysis of cellular images for identifying phenotypic changes is a key challenge within this strategy, and has recently seen promising progress with approaches based on deep learning. In this talk we describe our approaches based on deep multi-scale convolutional neural networks for phenotyping cellular images. We discuss supervised as well as unsupervised learning strategies, with the latter requiring no phenotypic labels for training. We present an example application based on images of E. Coli bacteria to show how we use machine learning to predict the binding preferences of antibiotics directly from microscopy image data.

3:30 Session Break

PERSONALIZED MEDICINE STRATEGIES FOR CLINICALLY ACTIONABLE DATA
153

3:40 Chairperson’s Remarks

Funda Meric-Bernstam, MD, Chair, Executive, Investigational Cancer Therapeutics, MD Anderson Cancer Center

3:45 Precision Oncology Decision Support

Meric-Bernstam_FundaFunda Meric-Bernstam, MD, Chair, Executive, Investigational Cancer Therapeutics, MD Anderson Cancer Center

Molecular profiling is increasingly utilized in the management of cancer patients. Decision support for precision oncology includes guidance of optimal testing, interpretation of test results including interpretation of functional impact of genomic alterations and therapeutic implications. We will review strategies for decision support and resources for identifying optimal approved or investigational therapies.

4:15 High-Performance Integrated Virtual Environment (HIVE) and BioCompute Objects for Regulatory Sciences

Mazumder_RajaRaja Mazumder, PhD, Associate Professor, Biochemistry and Molecular Medicine Georgetown Washington University

Advances in sequencing technologies combined with extensive systems level -omics analysis have contributed to a wealth of data which requires sophisticated bioinformatic analysis pipelines. Accurate communication describing these pipelines is critical for knowledge and information transfer. In my talk I will provide an overview of how we have been engaging with the scientific community to develop BioCompute specifications to build a framework to standardize bioinformatics computations and analyses communication with US FDA. I will also describe how BioCompute Objects (https://osf.io/h59uh/) can be created using the High-performance Integrated Virtual Environment (HIVE) and other bioinformatics platforms.

4:45 Integrating Genomic and Immunologic Data to Accelerate Translational Discovery at the Parker Institute for Cancer Immunotherapy

Wells_dannyDanny Wells, PhD, Scientist, Informatics, Parker Institute for Cancer Immunotherapy

Immunotherapy is rapidly changing how we treat both solid and hematologic malignancies, and combinations of these therapies are quickly becoming the norm. For any given treatment strategy only a subset of patients will respond, and an emerging challenge is how to effectively identify the right treatment strategy for each patient. This challenge is compounded by a concomitant explosion in the amount of data collected from each patient, from high dimensional single cell measurements to whole exome tumor sequencing. In this talk I will discuss translational research at the Parker Institute, and how we are integrating multiple molecular and clinical data types characterize the tumor-immune phenotype of each patient.

5:15 Close of Conference Program


Register