Cambridge Healthtech Institute’s Sixth Annual

Personalized Diagnostics

Impacting Care and Improving Outcomes

February 16-18, 2015 | Moscone North Convention Center | San Francisco, CA
Part of the 22nd Annual Molecular Medicine Tri-Conference


Now that the goal of moving NGS to the clinic has been accomplished, the next step is to ensure proper usage and adoption. Developing standards, protocols, robustness, cost-effectiveness and reimbursement of assays are all of prime importance. This year’s Personalized Diagnostics conference will review recent progress for building an infrastructure to incorporate the use of NGS and circulating biomarkers in the clinic for cancer, prenatal, cardiovascular, pediatric and genetic disease applications and illustrate value-added testing using case studies.

Scientific Advisory Board

Paul R. Billings, M.D., Ph.D., Chief Medical Officer, Thermo Fisher Scientific
Allan T. Bombard, M.D., MBA, Chief Medical Officer, Progenity, Inc.
German Pihan, M.D., Director, Hematopathology Lab, Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School
Karl V. Voelkerding, M.D., Professor of Pathology, University of Utah; Medical Director for Genomics and Bioinformatics, ARUP Laboratories

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Monday, February 16

10:30 am Conference Program Registration


11:50 Moderator’s Opening Remarks

Elaine Lyon, Ph.D., Medical Director, Molecular Genetics, ARUP (AMP 2014 President and Member, AMP Professional Relations Committee)

12:00 pm PANEL DISCUSSION: The Value of Molecular Diagnostics: A Discussion on Clinical Utility

The number and complexity of clinical molecular diagnostic tests (MDx) are increasing at a rapid rate. The health care professional asks: When does MDx make sense for my patient? What scientific evidence is needed to establish the clinical utility of a particular MDx? This keynote session will focus on the clinical utility of MDx in cancer and inherited disease. It is an outgrowth of ongoing discussions on this issue among members of the Association for Molecular Pathology. We will address the contribution of MDx to the care of patients at the present time, and anticipated progress in the near future.

  • Defining and measuring clinical utility from the point of view of both the clinician and the patient
  • MDx of malignancies to offer prognostic and predictive information useful for selecting the optimal therapy
  • Halting the “diagnostic odyssey” by selecting the appropriate genomic MDx for people, often children, with diseases that are difficult or sometimes seemingly impossible to diagnose
  • Establishing the value of MDx as a modality that will not only improve health-care, but do so in a way that will lower costs in the long run


Milena Cankovic, Ph.D., D(ABMLI), Director, Molecular Pathology and Genomic Medicine, Pathology, Henry Ford Hospital, Adjunct Assistant Professor, Wayne State University School of Medicine (AMP Clinical Practice Committee)

Paul G. Rothberg, Ph.D., Professor, Pathology & Lab Medicine, University of Rochester Medical Center (AMP Clinical Practice Committee, Genetics Subdivision Representative)

1:00 Session Break

1:15 Luncheon Presentation: Multiplexed Fusion Gene Detection with the nCounter ElementsTM Reagents

Gino Somers, Ph.D., Division Head, Pathology, The Hospital for Sick Children

nCounter Elements reagents enable the development of highly multiplexed assays capable of detecting fusion events.  Assays can be developed which target a given fusion gene without knowledge of the partner gene.  Alternatively, assays can be developed that target the unique sequence formed at the fusion junction.  These methods can be combined to develop robust, comprehensive assays for virtually any gene fusion.  Data will be presented demonstrating the performance of a comprehensive fusion gene assay based on nCounter Elements reagents.   

1:45 Session Break


2:30 Chairperson’s Remarks

Allan T. Bombard, M.D., MBA, Chief Medical Officer, Progenity, Inc.

2:40 History Before NIPT

Mark I. Evans, M.D., Professor, Obstetrics & Gynecology, Mount Sinai School of Medicine; Director, Comprehensive Genetics PLLC

The past 50 years have seen a pendulum of screening and testing for prenatal diagnosis with increasing rounds of sophistication, better statistics, and increasing acceptance. The “goal posts” have kept moving rendering sweeping conclusions as to primacy of any approach having a very short shelf life. The economics and science are intertwined in trying to determine optimal protocols and standards.

3:10 Case Studies in Prenatal Diagnostics; End-User of Prenatal Testing in Clinical Practice

Edward Wolf, M.D., President, New Jersey Perinatal Associates

To review the impact that rapid changes in prenatal testing options have had on the delivery of healthcare to pregnant women, from screening tests, ultrasound and cell free fetal DNA in maternal serum to invasive needle based testing options.

3:40 Lessons from NIPT: Interesting Cases, Complex Issues

Nicole Teed, MS, CGC, CEO, Integrity Genomics

In the few years since NIPT emerged as an advanced prenatal screening technology, a number of lessons have been learned, both biological and ethical. This presentation will use case studies to illustrate considerations for NIPT, with broader applications for other NGS technologies making their way into routine medical practice.

4:10 Changing the Landscape of Non-Invasive Prenatal Testing: The IONA Test 

Peter Collins, CCO, Premaitha Health

The first NIPT IVD combining the complexities of a NGS technology into a diagnostic kit that can be run in any clinical laboratory. IONA is designed to encourage broad uptake of the technology allowing all pregnant women accurate information about their pregnancy.

5:00 Plenary Session Panel 

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

7:30 Close of Day

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Tuesday, February 17

7:00 am Registration and Morning Coffee

8:00 Plenary Session Panel 

 9:00 Refreshment Break in the Exhibit Hall with Poster Viewing


10:05 Chairperson’s Remarks

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

10:15 Clinical Exome Sequencing for the Diagnosis of Neurodegenerative Disorders.

Rong Mao, M.D., Associate Professor, Pathology, ARUP Lab, University of Utah

Clinical exome sequencing is a new genome-based technology for demystifying undiagnosed illnesses - particularly rare childhood diseases. It has proven remarkably successful in identifying the causes of Mendelian diseases with a reported detection rate for deleterious mutations ranged from 25 to 30%. Herein I will present exome cases, and illustrate exome sequencing as an efficient diagnostic tool for complex neurodegenerative disorders.

10:45 Clinical Utility of Multiple-Gene Sequencing Panels for Hereditary Cancer Risk Assessment

James M. Ford, M.D., Associate Professor, Medicine & Genetics, Division of Oncology, Stanford University School of Medicine

Panels assaying multiple hereditary cancer risk genes are entering clinical use, however little is known about their yield or effect on clinical management of patients. We sequenced germline DNA samples from 400 patients with personal and family histories of breast and/ovarian cancer, but without BRCA1/2 mutations, and found ~10% carry potentially pathogenic mutations in other cancer susceptibility genes.

11:15 Applying Next-Generation Sequencing to Mutation Detection in Hematologic Malignancies with an Emphasis on Value Added to Patient Care

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

Genomic testing in hematologic malignancies reliably detects somatic mutations and can provide insight into disease development, prognosis and therapeutic options. This talk will discuss our approach to mutation detection in hematological malignancies, including capture of difficult to sequence regions (e.g. CEBPA and large FLT3-ITDs), and mutation profiles with respect to conventional cytogenetic findings. An overview of clinical impact of testing and case studies where our NGS-heme panel influenced treatment will be discussed.

11:45 Metagenomic Next-Generation Sequencing for Clinical Diagnosis of Infectious Diseases

Charles Chiu, M.D., Ph.D., Assistant Professor, Laboratory Medicine and Medicine/Infectious Diseases; Director, UCSF-Abbott Viral Diagnostics and Discovery Center; Associate Director, UCSF Clinical Microbiology Laboratory, UCSF School of Medicine

Metagenomic next-generation sequencing (NGS) is a powerful approach to diagnose infectious diseases by comprehensively detecting all potential pathogens in a single assay. We have validated an NGS assay for infectious diseases in a CLIA-certified laboratory setting that leverages a rapid, cloud-compatible bioinformatics pipeline for pathogen identification. We will discuss case studies applying this assay for diagnosis of challenging clinical cases in infectious disease.

12:15 pm Session Break

12:25 Luncheon Presentation: Information Innovation for Clinical Implementation of Next-Generation Sequencing

Shelly Gunn, M.D., Ph.D, CMO, MolecularHealth, Inc.

In-depth discussion of innovative clinico-molecular informatics platform that applies proprietary text analytics, biomedical curation, genome and proteome informatics and chemoinformatics methodologies to the analysis of patient-specific clinical and molecular information to identify the safest and most effective cancer treatment options. Case studies will be presented that demonstrate the translation of genetic tumor data to actionable information using HER2 positive early stage breast cancer cases.

12:55 Session Break 

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


2:00 Chairperson’s Remarks

Daniel H. Farkas, Ph.D., HCLD, FACB, Laboratory Director, Sequenom Center for Molecular Medicine

2:10 Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease

Atul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital; Co-Founder, Personalis and NuMedi.

Dr. Butte’s lab at Stanford builds and applies tools to translate more than a trillion points of molecular, clinical, and epidemiological data -- measured by researchers and clinicians over the past decade and now commonly called “big data”-- into diagnostics, therapeutics, and new insights into disease. Dr. Butte will highlight his lab’s work on using publicly-available molecular measurements to discover new diagnostics and treatment mechanisms for type 2 diabetes and the evaluation of patients presenting with whole genomes sequenced.

2:40 Adventitious Maternal Cancer Detection during Non-Invasive Prenatal Testing of Circulating Fetal DNA

Nilesh Dharajiya, M.D., Director, Clinical Lab, Sequenom Laboratories

Non-invasive prenatal testing of cell free DNA (cfDNA) provides a novel tool to detect chromosomal abnormalities prenatally. Maternal cfDNA is also sequenced, and therefore, we may learn about the mother’s genome or other medical conditions. Here, we provide an overview of cfDNA aneuploidy testing and present clinical cases where testing serendipitously detected cell free tumor DNA, resulting in an earlier diagnosis of a neoplastic process.

3:10 Liquid Biopsy Approaches For Detecting And Characterizing Human Cancer

Victor Velculescu, M.D., Ph.D., Professor, Oncology; Co-Director, Cancer Biology, Johns Hopkins Sidney Kimmel Cancer Center; Co-Founder, Personal Genome Diagnostics

Analyses of cancer genomes have revealed mechanisms underlying tumorigenesis and new avenues for therapeutic intervention. In this presentation, I will discuss lessons learned through the characterization of cancer genome landscapes, challenges in translating these analyses to the clinic, and new technologies that have emerged to analyze molecular alterations in the circulation of cancer patients as cell-free tumor DNA. These approaches have important implications for non-invasive detection and monitoring of human cancer, therapeutic stratification, and identification of mechanisms of resistance to targeted therapies..

3:40 The Hunt for Blood-Based Biomarkers for Diagnosis of Neurodegenerative Diseases

Robert M. Umek, Meso-Scale Diagnostics

While cerebrospinal fluid biomarkers and brain imaging have advanced our understanding of neurodegenerative diseases, there is considerable demand for blood-based biomarkers for diagnostics and use in clinical trials owing to the ease of sample acquisition and cost.  The status of the field as well as the challenges remaining will be considered.

3:55 Late Breaking Presentation

4:10 Mardi Gras Celebration in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall

This interactive session provides attendees an opportunity to choose a specific 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.

Relevance of Somatic Tumor DNA profiles to Germline DNA

James M. Ford, M.D., Associate Professor, Medicine & Genetics, Division of Oncology, Stanford University School of Medicine

  • Incidence of hereditary genetic changes in tumor genomes
  • How to interpret and follow-up somatic tumor profiles with germline DNA testing

Clinical Utility of NGS in Cancer: Measuring Outcomes

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

  • How best to capture clinical utility: changes in practice, outcomes or other mechanisms
  • Defining rare cancers based on mutation profiles
  • Mechanisms for pooling multi-institution data to define outcomes

Additional Roundtables to be Announced

6:00 Close of Day

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Wednesday, February 18

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Plenary Session Panel 

9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


10:35 Chairperson’s Remarks

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

10:45 Advancing Clinical Outcomes with Targeted Therapies for Patients with Solid Tumors Using the Next Generation Sequencing Assay

Jo-Anne Vergilio, M.D., Associate Medical Director, Foundation Medicine, Inc.

The FoundationOneTM assay for solid tumors has been validated as a sensitive comprehensive next generation sequencing assay that can detect all classes of genomic alterations at extremely low mutant allele frequencies. This presentation will highlight clinical applications of FoundationOne that have impacted disease outcomes in a variety of common and rare solid tumors.

11:15 High-Impact Applications of Liquid Biopsies

Luis A. Diaz, M.D., Associate Professor, Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center

Novel technologies to evaluate tumor burden in blood have opened the doors for several new clinical applications that will address unmet clinical needs in Oncology. This lecture will discuss these high-impact applications in the context of the most recent technologies.

11:45 The NGS Cost Equation in Cancer Care: Are We at the Tipping Point?

German Pihan, M.D., Staff Pathologist & Director, Hematopathology Lab, Pathology, Beth Israel Deaconess Medical Center

The cost-effectiveness of exome sequencing (WES) in the diagnosis, risk assessment and, particularly, therapy of cancer remains undetermined. This talk will address this very important issue and propose guidelines for the development of data-driven algorithms predicting cost-effective implementation of WES.

12:15 pm Enjoy Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


1:40 Chairperson’s Remarks

Paul R. Billings, M.D., Ph.D., CMO, Omicia, Inc.


Challenges Encountered Using NGS in Common Clinical Settings

Paul R. Billings, M.D., Ph.D., CMO, Omicia, Inc.

NGS is evolving to become a common part of oncology and obstetric practices as well as in the evaluation of pediatric and adult cases that are difficult to diagnose. A variety of challenges have been encountered in the high quality implementation of NGS in these settings. What do doctors and patients understand is the value of these tests and how does this impact consent for testing? What types of tests are ordered? What results are reported? What services optimize delivery? What interpretative support is required immediately and over time? Consultees will increasingly bring already captured NGS data to routine clinical encounters. This talk will discuss these issues as NGS is standardized and integrates in to professional medical practice.

2:20 Precision Prevention

Dietrich A. Stephan, Ph.D., Professor & Chairman, Human Genetics, University of Pittsburgh; Associate Director, Population Genetics and Translational Acceleration, Institute for Personalized Medicine of UPMC & University of Pittsburgh Health

New molecular diagnostics are allowing us not only stratify individuals for therapies when sick (personalized medicine), but also now to allow pre-symptomatic molecular diagnosis. Precision prevention promises to significantly impact individual outcomes and improve public health.

2:50 Delivering Diagnostic and Predispositional Genomic Findings in the Clinic

Robert C. Green, M.D., MPH, Associate Professor, Medicine & Genetics, Brigham & Women’s Hospital and Harvard Medical School

This talk will describe empirical efforts to use genomic information from germline sequencing in the clinical practice of medicine. Evidence will be presented emphasizing distinctions between sequencing for diagnosis and predispositional or predictive testing. New data will be presented supporting the penetrance of incidental findings in unselected populations.

Genomic Healthcare3:20 The Clinical and Diagnostic Advantages of Genome-Wide Sequencing Based MDx

Elizabeth Worthey, Ph.D., Vice President, Informatics, Genomic Healthcare Innovations

Many patients with suspected genetic disorders remain undiagnosed and at risk for inappropriate, costly therapies that may negatively impact quality of life. We will discuss how genome-wide sequencing based tests can significantly increase the definitive diagnosis rate for these patients.

3:35 Late Breaking Presentation

3:50 Refreshment Break


4:00 Chairperson’s Remarks

Chris Willis, Ph.D., Manager, Discovery Solution Scientists, IP & Science, Thomson Reuters


Global Exchange of Human Genetic Data for Medicine and Research

David Haussler, Ph.D., Distinguished Professor and Scientific Director, UC Santa Cruz Genomics Institute, University of California Santa Cruz

Every human disease is a rare disease at the molecular level. No single institute has enough patients to understand any particular molecular subtype. For genomics to benefit medicine and science, we must share data. This presentation outlines the data standards and Application Programming Interfaces developed by the Global Alliance for Genomics and Health that are intended to address this issue, and highlight a few global genomics projects that use them.

4:40 Data Linking and Warehousing to Support Evaluation of Pathogenicity of Genes and Genetic Variants by the Clinical Genome Resource Project

Xin Feng, Ph.D., Assistant Professor, Bioinformatics Research Lab and Department of Molecular and Human Genetics, Baylor College of Medicine

The Clinical Genome Resource (ClinGen) is an NIH-funded program dedicated to creating a database of clinically relevant genomic variants to inform genome interpretation in a variety of clinical contexts. A core component of ClinGen is ClinGenDB, an integration point for data about variants that supports their computational and manual evaluation by experts. The variant data is integrated from clinical and research databases, including several genomics initiatives. Data Warehousing is the traditional approach to data integration that brings all the relevant data physically together. Data Linking is a new approach to data integration that uses new web standards such as JSON-LD, RDF, and Linked Data Platform 1.0 to integrate data across distinct physical locations. In this presentation, we compare the two approaches by going through a number of use cases of data integration in ClinGenDB for the purpose of evaluating pathogenicity of genetic variants.

5:10 XPRIZE: Transforming Science Fiction into Science Reality through Incentivized Competition

Grant Campany, Senior Director, XPRIZE

Imagine a portable, wireless device in the palm of your hand that monitors and diagnoses your health conditions. That’s the technology envisioned by the $10 million Qualcomm Tricorder XPRIZE competition, and it will allow unprecedented access to personal health metrics. The end result: Radical innovation in healthcare that will give individuals far greater choices in when, where, and how they receive care.

5:40 Close of Conference Program

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

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