Cambridge Healthtech Institute’s Eighth Annual

Personalized Diagnostics

What Can NGS Bring to Medicine?

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


NGS and other molecular tools are being employed for opportunities enabled by immuno-oncology, liquid biopsy and combination therapy. The Eighth Annual Personalized Diagnostics conference will offer practical insights for building gene panels, understanding the changing landscape of reimbursement and regulation, and deploying clinical sequencing for immunotherapy, liquid biopsy and a host of diseases not limited to oncology. Recently uncovered genetic mutations in a patient's own cancer can guide a personalized treatment strategy. Plan to attend and learn what is being done to further our understanding of disease and combat it with targeted approaches.

Scientific Advisory Board

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

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

Karl V. Voelkerding, M.D., Professor, Pathology, University of Utah; Medical Director for Genomics and Bioinformatics, ARUP Laboratories

Monday, February 20

10:30 am Conference Program Registration Open


11:50 Chairperson’s Opening Remarks

Trevor W. Brown, MSc, Vice President, Precision Medicine, SeraCare Life Sciences, Inc.

12:00 pm Making Omic Data Clinically Actionable

Elizabeth Worthey, Ph.D., Faculty Investigator, Clinical Informatics Director, and Adjunct Associate Professor, Software Development and Informatics, Pediatrics and Genetics, HudsonAlpha Institute for Biotechnology

The American College of Medical Genetics and Genomics (ACMG), the Association for Molecular Pathology (AMP), and the College of American Pathologists (CAP), recently developed guidelines to standardize interpretation and reporting of genomic test results. Their assessment ultimately ended up producing twenty-eight such weighted criteria as well as suggesting the methods through which they could be combined in order to derive the reporting category.

12:30 Scalable Approach for Continuous Analysis of Exome Sequencing Data

Avni Santani, Ph.D., Director, Division of Genomic Diagnostic, The Children’s Hospital of Philadelphia; Assistant Professor, Clinical Pathology and Laboratory Medicine, University of Pennsylvania

With the explosion of genomic information and novel gene discoveries, clinical laboratories are faced with critical challenges in data interpretation. For complex genetic tests such as exome sequencing in pediatric population, the clinical presentation of patient continues to evolve, therefore affecting the phenotype driven analysis of genomic data. Using clinical cases as examples, this presentation will address these challenges and propose strategies that clinical laboratories can utilize for re-analysis of genomic data in exome sequencing.

1:00 Session Break

1:10 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

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

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

10:15 Validation and Accumulated Experience with Large Gene Panel for the Detection of Somatic and Inherited Cancer Gene Mutations

Colin Pritchard, M.D., Ph.D., Associate Professor, Laboratory Medicine, University of Washington

Genomic sequencing technology is transforming cancer diagnostics by enabling tumor-based mutation profiling for precision cancer therapy. Since 2011, the University of Washington has offered large panel genetic testing for both cancer predisposition and for somatic mutation profiling in tumors. This presentation will review our experience with clinical next-generation sequencing-based panels for cancer including aspects of assay validation, bioinformatics infrastructure, interplay between somatic and germline findings, and interpretation and reporting.

10:45 Enabling a Genetically Informed Approach to Cancer Medicine: Evaluation of the Impact of a Comprehensive Tumor Sequencing Panel

Douglas B. Johnson, Ph.D., Assistant Professor, Medicine, Vanderbilt University Medical Center

Next-generation sequencing profiling is widely used to identify actionable genetic alterations in solid tumors. We reviewed our experience using a sequencing platform of 236-315 genes (FoundationOneTM, Foundation Medicine), and found that most patients (83%) had potentially actionable genetic changes, and 21% of these received genotype-directed treatments. We also observed that total number of mutations identified strongly correlated with response to anti-PD-1 directed therapies in melanoma.

11:15 NGS-Based Panel Testing for Hematologic Malignancies

Frank C. Kuo, M.D., Ph.D., Director, Assay Development, Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women’s Hospital

Genomic profiling plays an increasingly important role in the diagnostic workup for patients with hematologic malignancies. Recurrent mutations occur in a few dozen genes involved in signal transduction, splicing, DNA methylation, and transcription regulation with implication in therapeutic decisions and prognosis. An NGS-based panel can provide comprehensive mutational profile in a timely and cost-effective manner and are likely to become an indispensable tool in evaluation of patients with hematologic malignancies.


12:15 pm Session Break

12:25 Luncheon Presentation I: FibroTx TAP and SELF: Pioneering the Potential of Topical Skin-Biomarkers for Personalized Care

Pieter Spee, CTO, FibroTx LLC

FibroTx has developed two platform technologies for non-invasive measurements of protein biomarkers directly from skin. TAP allows unique opportunities for product development and biomarker research. SELF is the first practical molecular point-of-care device intended for personalised skin care.

12:55 Luncheon Presentation II (Sponsorship Opportunity Available)

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


2:00 Chairperson’s Remarks

Avni Santani, Ph.D., Director, Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia

2:10 Tumor Heterogeneity and Mutational Shift: Monitoring Mutations throughout the Course of Their Disease

Jennifer J.D. Morrissette, Ph.D., Clinical Director, Center for Personalized Diagnostics, University of Pennsylvania

Next-generation sequencing has become routine in the diagnosis and subsequent disease monitoring of cancer patients. Hematological malignancies are regularly monitored at diagnosis and at interim follow-ups by NGS using a custom hematological-NGS panel and chromosome analysis to monitor treatment response. This talk will present our experience in tracking the mutational landscape in the context of therapy and disease state.

2:40 PhenoDB and GeneMatcher, Solving the Molecular Basis of Mendelian Phenotypes

Nara Lygia de Macena Sobreira, M.D., Assistant Professor, Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University

To facilitate data sharing as well as improve the search for patients or model organisms with variants in specific candidate genes, we have added capabilities to PhenoDB ( and GeneMatcher ( As of September 2016, 5,209 genes were submitted by 2,131 individuals from 57 countries and generated 8,986 matches that have enabled collaborations and the description of novel Mendelian phenotypes and novel Mendelian genes.

3:10 Leveraging Long Read Technologies for Developing Niche Assays with Diagnostic Potential

Robert P. Sebra, Ph.D., Director, Technology Development, Icahn Institute of Genomics & Multiscale Biology; Associate Professor, Genetics & Genomics, Icahn School of Medicine at Mount Sinai

To address technologic limitations and provide a comprehensive assessment of genome variation associated with disease, we employed SMRT sequencing technology to access previously unresolvable genomic regions through unbiased, long read sequences spanning thousands of basepairs. Given these capabilities to comprehensively assess variation using long reads in pathologically relevant regions in support of clinical thinking, the potential exists to characterize health of an individual at a deeper level than previously possible.

Omicia3:40 Increasing Diagnostic Yield in Whole Genome Interpretation Using Omicia’s Opal Clinical Platform

Charlene Son Rigby, MBA, Vice President, Products and Strategy, Omicia

linical NGS testing is expanding to exomes and genomes. Omicia's algorithms, VAAST and Phevor, quickly rank disease-causing candidates based on impact and relationship to phenotype, thereby accelerating interpretation and reporting. We highlight our work on Genomics England's 100,000 Genomes Project.

3:55 Sponsored Presentation (Opportunity Available);

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.

Making Omic Data Clinically Actionable

Elizabeth Worthey, Ph.D., Faculty Investigator, Clinical Informatics Director, and Adjunct Associate Professor, Software Development and Informatics, Pediatrics and Genetics, HudsonAlpha Institute for Biotechnology

The Science & Art of Training and Validating Molecular Classifiers

Morita Pagan, Ph.D., Principal Science Advisor and Founder, MP Consulting


  • Sample selection and clinical data curation
  • Cohort balancing
  • Iterative testing and algorithm lock


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

Karl V. Voelkerding, M.D., Professor, Pathology, University of Utah; Medical Director for Genomics and Bioinformatics, ARUP Laboratories

11:00 The SPOT/DX Diagnostic Quality Assurance Pilot: An Update

John Pfeifer, M.D., Ph.D., Vice Chair, Clinical Affairs, Pathology, Washington University School of Medicine

The Sustainable Predictive Oncology Therapeutics and Diagnostics (SPOT/Dx) working group has launched a Diagnostic Quality Assurance Pilot designed to develop performance standards, consensus quality control materials, and a transparent pre-market approach to ensure that labs demonstrate their ability to accurately determine the sequence of clinical decision parameters (i.e., genes) regardless of whether they are using an FDA-approved in vitro companion diagnostic (IVD) or a laboratory-developed test (LDT).

11:20 Developing Standards for NGS-Based Testing in the Evolving Regulatory Environment

Birgit H. Funke, Ph.D., FACMG, Associate Professor, Pathology, MGH/Harvard Medical School; Director, Clinical Research and Development, Laboratory for Molecular Medicine, Partners HealthCare

The complexity and scope of molecular diagnostic testing has dramatically increased and requires not only substantial knowledge and expertise, but also an evolving framework for test design, validation and implementation. This presentation will discuss evolving frameworks for developing standards to meet the increasing demand for enhanced guidance and to enable standardization of molecular testing cross laboratories.

11:40 Regulation and Reimbursement of Genomic Tests: Challenges and Solutions

Girish Putcha, M.D., Ph.D., Director, Laboratory Science, Palmetto GBA (MolDX)

The regulatory and reimbursement environment today for genomic tests is in seemingly constant flux. This presentation will review some of the structural challenges with the diagnostics ecosystem and propose some solutions.


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 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

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