Cambridge Healthtech Institute’s Tenth Annual

Clinical NGS Diagnostics

Translating Genomic Data to the Standard of Care

February 20-22, 2017 | Moscone North Convention Center | San Francisco, CA
Part of the 24th International Molecular Medicine Tri-Conference


Clinical sequencing is paving the way for the application of molecular diagnostics in infectious disease, newborn medicine, cancer, autoimmune, genetic and immunotherapy. Many of these applications were formerly intractable, requiring an odyssey of trial and error over weeks or months and at great expense. Now a myriad of tools is being used to enable accurate and rapid diagnosis and is allowing new treatments. The Clinical NGS Diagnostics track will feature novel technologies available for clinical use along with validation, implementation and standardization protocols for sequencing.

Monday, February 20

10:30 am Conference Program Registration Open


11:50 Chairperson’s Opening Remarks

Andrew Bryan, M.D., Ph.D., Acting Assistant Professor, Assistant Director, Clinical Microbiology, Department of Laboratory Medicine, University of Washington

12:00 pm Emerging Assays for Infectious Diseases in Diagnosis and Outbreak Surveillance

Charles Chiu, M.D., Ph.D., Associate Professor, Lab Medicine and Infectious Diseases; Director, UCSF-Abbott Viral Diagnostics and Discovery Center; Associate Director, Clinical Microbiology Laboratory, University of California, San Francisco

Advances in technology, genomics, and bioinformatics and the vast increases in the size of reference databases have made comprehensive diagnosis of infectious diseases practical. Here we will discuss the promise, challenges, and experience with clinical validation and implementation of a metagenomic next-generation sequencing (mNGS) assay for identification of pathogens in hospitalized patients. We will also discuss the use of new technologies, including nanopore sequencing and transcriptome profiling, for surveillance of epidemics such as the 2015-2016 Zika virus outbreak in the Americas.

12:30 Implementation of Metagenomic Next-Generation Sequencing for Pathogen Detection in the Clinical Laboratory

Samia Naccache, PhD, Clinical Microbiology Fellow, Pathology and Lab Medicine, Children’s Hospital Los Angeles

Metagenomic next-generation sequencing (mNGS) for pathogen detection allows for unbiased identification of infectious agent nucleic acid in clinical samples. We have implemented this assay in the UCSF clinical laboratory for diagnosis of meningitis / encephalitis using optimized library preparation and bioinformatics processing steps, with case discussion and decision support through the Microbial Sequencing Board. This talk will outline the mNGS assay performance, clinical utility and effect on patient management decisions.

1:00 Session Break

Fry_Labs1:10 Luncheon Presentation: Years On the Bench: Design and Implementation of a Microbial NGS Clinical Diagnostics System

Jeremy Ellis, Ph.D., Research Director, Laboratory Manager, Research & Development, Fry Laboratories, LLC

Translating research-based NGS methods into the clinical diagnostics laboratory poses several unique challenges. Experience with a microbial NGS diagnostics assay will be reviewed in addition to design requirements. Our system, RIDI™, will be used to explore challenges and opportunities.

2:10 Session Break


2:30 Chairperson’s Remarks

German Pihan, M.D., Director, Hematopathology Lab, Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School

2:40 Profiling of Exhausted T Cells in Tumors Predicts PD-1 Response

Kelly Mahuron, M.D., Resident, School of Medicine, University of California, San Francisco 

Immune checkpoint blockade is revolutionizing therapy for advanced cancer. However, many patients do not respond to treatment. The identification of robust biomarkers that predict clinical response to specific checkpoint inhibitors is critical in order to stratify patients and to rationally select combinations in the context of an expanding array of therapeutic options. We performed multi-parameter flow cytometry on freshly isolated metastatic melanoma samples prior to treatment and correlated subsequent clinical response with tumor immune phenotype.

3:10 Defining Immunoglobulin Somatic Hypermutation in de novo Diffuse Large B-Cell Lymphoma Patients: Potential Application for Prognosis and Risk Stratification

Ken H. Young, M.D., Ph.D., Professor, Hematopathology, The University of Texas MD Anderson Cancer Center

Characterization of immunoglobulin gene helps to identify cell-of-origin of mature B cell malignancies such as chronic lymphocytic leukemia, whereas its role in the pathogenesis of DLBCL is poorly understood. In this study, we studied molecular repertoire of both immunoglobulin heavy- and light-chain genes in a large cohort of de novo DLBCL patients using high-throughput next generation sequencing (NGS).

3:40 High-Throughput TCR Sequencing Provides Added Value in the Diagnosis of Cutaneous T-Cell Lymphoma

Thomas S. Kupper, M.D., Chair, Dermatology, Brigham and Women’s Hospital; Dana Farber Cancer Institute; Thomas B. Fitzpatrick Professor, Harvard Medical School

Cutaneous T Cell Lymphomas (CTCL) are the most common extranodal non-Hodgkins T cell lymphomas. The diagnosis can be difficult and delayed (avg 5-6 years), as the lesions resemble inflammatory skin disorders. Unlike PCR-based clonality assays, high throughput sequencing of the TCR genes yielded a 100% sensitivity for detection of a clonal T cell population in CTCL lesions. HTS can also be used to assess response to therapy.

Genoptix4:10 Automation of NGS-Data Analysis and Interpretation in a High-Throughput Clinical Setting

Matthew McGinniss, Ph.D., FACMG, Executive Director, Clinical Genomics, Genoptix Medical Laboratory

 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

Karen A. Heichman, Ph.D., Vice President, Director, PharmaDx Program, ARUP Laboratories; Pathology, University of Utah

10:15 The FDA Review Process for Companion Diagnostic Devices

Soma Ghosh, Ph.D., Scientific Reviewer, FDA/CDRH/OIR/DMGP

Companion diagnostics have emerged as a powerful tool in personalized medicine allowing treatment decisions to be tailored for each patient. They are essential for the safe and effective use of many emerging and established therapeutic products, and promise a clearer understanding of disease development at the individual level. In the light of their expanding role in clinical decision making, my talk will focus on the critical regulatory review elements that FDA considers when evaluating companion diagnostic devices. I will illustrate key points using recent approvals as examples.

10:45 ARUP Laboratories’ Experience with FDA Approval of Companion Diagnostic (CDx) Tests within the Clinical Laboratory Environment

Karen A. Heichman, Ph.D., Vice President, Director, PharmaDx Program, ARUP Laboratories; Pathology, University of Utah

In December 2015, ARUP Laboratories received FDA approval for two CDx tests for Gleevec eligibility: KIT D816V Mutation Detection by PCR and PDGFRB FISH. These two tests are performed exclusively by ARUP as required under HDE regulations. ARUP established an augmented quality system integrated within the CLIA environment, which meets FDA requirements for medical devices, including a design control program. This presentation will address ARUP’s successful approach to CDx development.

11:15 Regulatory Pathways for NGS Applications and Other Advanced Technologies

Pamela Swatkowski, Director, Regulatory Affairs, Abbott Molecular

11:45 Panel with Session Speakers

12:15 pm Session Break

12:25 Luncheon Presentation I: Tackling the Challenge of FFPE DNA Extraction: An Automation Ready Solution Designed with an NGS Focus

Jennifer MacFarland, Field Marketing Manager, Automation and Genomics, Beckman Coulter Life Science

FormaPure DNA provides an automation-ready, SPRI-based extraction reagent kit to support your evolving research needs. Most notably, it provides significant time savings in reduced turnaround times and less than 15 minutes of hands-on time when automated on a Biomek.

12:55 Luncheon Presentation II (Sponsorship Opportunity Available)  

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


2:00 Chairperson’s Remarks

Patrick Hurban, Ph.D., Senior Director and Global Head, Translational Genomics, Q Squared Solutions

2:10 Choosing an Effective Validation Plan for NGS Assays in Oncology

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

The analytical validation of an NGS assay for the most part determines the reliability of results and therefore dictates the effectiveness of the assay for management of the cancer. As the number of laboratories offering NGS tests in oncology increases, the need for recommendations and guidelines that address the processes of assay validation are noteworthy. Several organizations and regulatory bodies have been working on developing documents to help and guide laboratories plan and execute the validation of NGS assays for oncology. In this presentation, we will discuss the validation prerequisites that are important and need to be addressed for implementing a reliable and useful NGS assay for oncology.

2:40 Towards Implementation of NGS as Clinical Assay: FFPE Pre-Analytical Optimization and Analytical Consideration in WES Commercial Lab Selection

Ping Qiu, Ph.D., Translational Molecular Biomarkers (TMB), Genomics, Merck Research Laboratories

Higher non-synonymous mutational burden assessed by whole exome sequencing in tumors is associated with durable clinical benefit in immune checkpoint inhibitors treatment. Cancer genome WES poses a unique challenge due to limited tissue, tumor heterogeneity and sequencing artifacts introduced by FFPE tissue. Multiple genomics CROs were assessed on their NGS pre-analytics and the quality of WES data generated. Recommendations are made on FFPE WES pre-analytics and data interpretation.

3:10 Genotyping in an HTP Drug Development Pipeline: Tough Assays, High Sample Numbers, and Ever-Changing Goals

J. Colin Cox, Ph.D., Science Manager, Genentech

Deborah Siler, Ph.D., Senior Research Associate, Mouse Genetics, Genetech

We use “acoustic droplet ejection” (ADE) to perform high-throughput genotyping in the context of an R&D biotherapeutics pipeline. Our lab processes roughly 350,000 samples a year in order to generate ~800,000 genotypes on very complex genetic models. Recently, we validated a no-downtime upgrade from traditional pipetting robots to ADE dispensers and investigated the effect on cross-contamination and return-on-investment.

SeraCare3:40 Real-World Examples of Validating a Cancer Sequencing Assay: Case Example, RNA Fusions

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

Laboratories have difficulties reconciling vague guidelines against sample scarcity and budget limits. How can labs validate and implement cancer assays? Materials to implement robust and reliable assays and software to track and trend data over time will be presented.

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

Stephen F. Kingsmore, MB, ChB, BAO, DSc, FRCPath, President and CEO, Rady Pediatric Genomics & Systems Medicine Institute, Rady Children’s Hospital, San Diego

11:00 Genomic Sequencing of Healthy and Sick Newborns in the BabySeq Project

Joel Krier, M.D., MMSc, Clinical Chief, Division of Genetics; Director, Brigham Genomic Medicine, Brigham and Women’s Hospital; Instructor, Harvard Medical School

The BabySeq Project is a proof-of-concept randomized control trial examining the implications of genomic newborn sequencing (gNBS) in two populations: a) sick or premature neonates admitted to the Boston Children’s Hospital and Brigham and Women’s Hospital (BWH) ICUs and b) generally healthy neonates from the BWH well nursery. This presentation will summarize the key progress and findings to date including study design, implementation, and preliminary results.

11:30 Ethical and Social Challenges Associated with Sequencing Newborns

Don Bailey, Ph.D., Distinguished Fellow, RTI International

Next-generation sequencing offers the promise of potentially useful health information but also evokes a number of ethical and social challenges. I describe a few of the major concerns, summarize what is known about each, and suggest strategies by which each could be mitigated.

12:00 pm Exome Sequencing of Newborn Dried Blood Spots: Implications for Newborn Screening and for Exome Diagnostics

Steven E. Brenner, Ph.D., Professor, Plant & Microbial Biology, University of California, Berkeley

Public health newborn screening (NBS) identifies newborns with rare treatable conditions, permitting early intervention. The NBSeq project is evaluating the potential of whole exome sequencing in NBS using de-identified, archived dried blood spots (DBS) under an IRB-approved protocol with the California Department of Public Health. One aim explores feasibility of WES to replace or augment MS/MS for metabolic disorders. DBS of all California newborns from Jul 2005–Dec 2013 with disorders diagnosed by MS/MS and a selection of false positives were made available (1600 samples) and are being studied.

12:30 Session Break

12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

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


1:50 Chairperson’s Remarks

Luis A. Diaz, M.D., Head, Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center

2:00 Genomic Features of Resistance to Anti-PD-1 Immunotherapy

Jesse Zaretsky, UCLA-Caltech Medical Scientist Training Program, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles

Resistance to anti-PD1 immunotherapy can take the form of either innate lack of response, or late acquired resistance after initial tumor regression. For the former, we define a transcriptomic mesenchymal and wound-healing associated expression signature enriched among non-responders in pre-therapy tumors from metastatic melanoma patients. For the latter, exome sequencing of paired pre/post relapse tumors revealed loss of function mutations in the interferon response pathway and antigen presentation machinery.

2:30 Shaping of Immunotherapy Response by Cancer Genomes

Rajarsi Mandal, M.D., Head & Neck Surgical Oncology Fellow; Professor, Surgery, Memorial Sloan Kettering Cancer 

Immune checkpoint blockade is a promising approach for the treatment of human malignancies. For example, treatment of patients with advanced lung cancers and melanoma have resulted in improved response rates and durable disease control. However, the extent to which patients derive benefit is diverse and the determinants that drive response to therapy are ill-defined. We have sought to define the genomic determinants of response to immune checkpoint blockade therapies such as anti-CTLA-4 and anti-PD-1. Our work has shown that tumor mutational burden, clonality, and mutational landscape features help dictate clinical response. Mutations in genes that are part of the antigen presentation machinery are rare but can be preferentially downregulated in tumors. Reexpression of genes in the MHC antigen presentation pathway by treatment with epigenetic therapy synergizes with immune checkpoint blockade to boost anti-tumor responses.

3:00 Addressing the Challenges Associated with Immuno-Therapy Biomarker Testing

John Leite, Ph.D., Vice President, Oncology, Market Development & Product Marketing, Illumina, Inc.

Recent developments in immuno-therapy have yielded exciting and promising results, but have also highlighted the need for effective predictive solutions. In this session, we will discuss the inherent testing challenges facing translational researchers, and future challenges facing clinicians seeking to implement these solutions into routine clinical practice.

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 Talk Title to be Announced

Amado Zurita-Saveedra, M.D., Associate Professor, MD Anderson

5:15 Close of Conference Program

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