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Cambridge Healthtech Institute’s Third Annual

Clinical Sequencing

Translating NGS to Practice

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


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

Monday, February 16

10:30 am Conference Program Registration


11:50 Chairperson’s Opening Remarks

Steffan N. Ho, M.D., Ph.D., Senior Director, Early Development and Translational Oncology, Pfizer Oncology

12:00 pm LungMAP/S1400: A Unique Public-Private Master Protocol for Drug-Biomarker Registration

David Gandara, M.D., Professor of Medicine, Division of Hematology/Oncology, University of California, Davis School of Medicine; Director, Thoracic Oncology Program, Senior Advisor to the Director, UC Davis Comprehensive Cancer Center; Chair, Lung Committee, Southwest Oncology Group (SWOG)

Despite rapid advances in deciphering the complex genomics of non-small cell lung cancer (NSCLC), clinical translation into approvable biomarker-drug combinations has been problematic, due in part to the relative rarity of genomically-defined subsets. Lung-MAP (S1400) is a one-of-a-kind public-private partnership designed to speed up development of targeted therapies for NSCLC of squamous cell histology (SCCA). Here we describe development of this registration-compliant biomarker-driven Phase II/III multi-arm “master” protocol, employing next generation sequencing to identify actionable molecular abnormalities, followed by patient randomization to biomarker-driven targeted therapy versus standard of care.

12:30 The Evolving Genotype-to-Phenotype Paradigm in Oncology Drug Development

Steffan N. Ho, M.D., Ph.D., Senior Director, Early Development and Translational Oncology, Pfizer Oncology

The clinical application of multiplexed molecular profiling technologies offers unprecedented opportunities to enhance the drug development process by directing treatment to patients who are more likely to benefit. However, molecular profiling technologies are in the early stages of clinical application as companion diagnostic tests. Future success will require close integration between not only biology and technology, but also between clinical and diagnostic development strategies.

1:00 Enjoy Lunch on Your Own


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 Associate.

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.

4:40 Break and Transition to Plenary Session

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

2:10 Validation Challenges for Panels and Exomes

Josh Deignan, Ph.D., Associate Director, UCLA Molecular Diagnostics Laboratories, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA

Guidelines for the validation of molecular diagnostic tests have existed for some time, but guidelines for NGS testing have only recently emerged. Moreover, the approach required for the validation of a NGS mutation panel is different than the one required for an exome sequencing test, both of which are now offered clinically at UCLA. This talk will discuss our experiences with the validations of these two types of NGS tests.

2:40 FDA-Approved Versus LDT-Based NGS Systems: Preanalytical Issues and Validation

Jamie L Platt, Ph.D., Vice President, Genomic Solutions, Molecular Pathology Laboratory Network, Inc.

As NGS technologies have matured and their utility in clinical diagnostics has been embraced, the evolution of RUO-based Laboratory Developed Processes (LDPs) to FDA-Cleared In Vitro Diagnostic Tests has followed. The major considerations around Preanalytical issues for these two categories of systems will be compared and discussed. In addition, the key validation or verification challenges will be contrasted and discussed within the context of a CLIA Lab experience using both types of systems. The objective of the presentation is to provide sufficient information, drawn from experience, to enable labs to choose the path that best suits their environment, goals and objectives.

3:10 PANEL DISCUSSION: Comparing Major NGS Instruments: Technical Differences, Application Preferences

Moderator: Jamie L Platt, Ph.D., Vice President, Genomic Solutions, Molecular Pathology Laboratory Network, Inc.

Panelists: Shelly Gunn, M.D., Ph.D., CMO, Molecular Health

Martin Siaw, Ph.D., MB (ASCP), Associate Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute

Selecting the NGS platform or platforms that best address the pre-analytical and technical considerations of the assay objectives given the specific environment can be a challenging undertaking. Platform throughput, chemistry, and error modality vary greatly and are tightly tied to overall assay performance. This discussion will focus on the strengths and capabilities of the different commercially available NGS platforms from the perspective of users with experience on multiple platforms.

3:40 A Novel Method for Efficiency and Hands-Free Purification of Circulating, Cell-Free DNA (ccfDNA) from Human Plasma

Douglas Horejsh, Ph.D., Senior Research Scientist, Promega Corporation

The Promega Maxwell® RSC circulating DNA kit allows parallel purification of ccfDNA from 1-16 plasma samples. This method purifies high-quality DNA suitable for use in qPCR and NGS. The absence of pre-processing steps improves reproducibility and lowers risk of contamination.

3:55 Can You Handle a Million Tests per Year? Transitioning from Clinical Trials to a Validated, High-Throughput Diagnostics Operation

Daniel Steenblik, Vice President of Technology and Operations, Engineering, sampleminded

We will discuss the challenges of transitioning a lab from clinical trials to a high throughput diagnostic organization. How we employ a simple and sleek mission critical LIS, including tablets, monitoring and workflow metrics to capture quality indicators, while maintaining traditional LIS/LIMS functionality.

Mardi Gras4:10 Mardi Gras Celebration 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.

Integration of Various Laboratory Data into Genomic Data Analysis

Peter L. Nagy, M.D., Ph.D., Assistant Professor, Pathology and Cell Biology; Director, Clinical Next-Generation Sequencing, Laboratory of Personalized Genomic Medicine


  • Database architecture to maximize sensitivity and specificity for detection of previously reported pathogenic variants
  • How to identify novel pathogenic variants
  • How to follow up on novel potentially pathogenic variants


Future of Portable Sequencing for Real-Time Diagnostics

Kamlesh Patel, Ph.D., Manager, Advance Systems Engineering and Deployment, Sandia National Labs


  • Discuss the the current state-of-the-art of the technology and current limitations
  • Explore the diagnostic landscape in search of the right applications for portable sequencing
  • Predict how diagnostics would change with this technology 5 years from now.


NGS Assay Development and Validation

Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Molecular Pathology Laboratory Network, Inc


  • NGS clinical test requirements – panels vs exomes/genomes
  • Development and validation of germline clinical NGS tests
  • Development and validation of somatic clinical NGS tests


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.

1:50 Keynote Presentation: 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, Director, G2P Research Program; Associate Director, Research, Partners Personalized Medicine, Division of Genetics, Department of Medicine, Brigham and 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.

3:20 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.  

3:50 Refreshment Break

Advances in Computational
Cancer Genomics

4:00 Chairperson’s Remarks

Andreas Scherer, Ph.D., President and CEO, Golden Helix

4:10 Bioinformatics of Cancer Gene Panels: Challenges to Creating Effective Testing Workflows

Andreas Scherer, Ph.D., President and CEO, Golden Helix

In the transition of NGS to a clinical setting, the cancer gene panel is leading with a clear value proposition of clinically actionable results in a simple package. Except it’s not so simple. In this presentation I will cover the bioinformatics tools and best practices to achieve the goal of a reproducible workflow for analyzing NGS gene panel data. From amplicon and sample QC, to annotation sources and filtering thresholds, to summary of therapeutic targets and gene level reports, I will cover the methods and edge cases that go into setting up a gene panel test.

4:40 Maximizing the Utility of TCGA Genomic Data: Tools, Analysis and Discovery

Han Liang, Ph.D., Assistant Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas, MD Anderson Cancer Center

A central question for the cancer research community is how to use these genomic and proteomic data. I will first introduce two useful bioinformatics tools we recently developed for effectively analyzing and visualizing TCGA data: SurvNet and TCPA. Then I will present a systematic evaluation of the power of diverse TCGA molecular data with or without clinical variables in predicting patient survival and discuss the potential utility of cross-tumor analysis. Finally, I will focus on the biomedical significance and clinical relevance of expressed pseudogenes in human cancer.

5:10 Characterization of Cancer Genomes

Sohrab Shah, Ph.D., Assistant Professor, Pathology and Computer Science, University of British Columbia; Scientist, BC Cancer Agency

5:40 Close of Conference Program

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