Cambridge Healthtech Institute’s Ninth Annual

Clinical NGS Diagnostics

Translating Genomic Data to the Standard of Care

March 7 – 9, 2016 | Moscone North Convention Center | San Francisco, CA
Part of the 23rd International Molecular Medicine Tri-Conference


Monday, March 7

10:30 am Conference Program Registration Open


11:50 Chairperson’s Opening Remarks

Stephen Salipante, M.D., Ph.D., Assistant Professor, Director, Next-Generation Sequencing Analytics Laboratory; Assistant Director, Molecular Diagnosis Section, University of Washington

12:00 pm NGS Assays for Diagnosis of Infectious Diseases

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

There is great interest and potential in the use of metagenomic next-generation sequencing (NGS) for diagnosis of infectious diseases in clinical settings. We will discuss assay development, clinical validation, bioinformatics analysis, and regulatory considerations involved when developing such NGS-based assays in CLIA-certified laboratories. We will also discuss emerging rapid, point-of-care sequencing technologies and host-based approaches for infectious disease diagnosis.

12:30 Ingredients for a CLIA-Approved Clinical 16S rRNA Gene Assay for Mixed Bacterial Populations by Next-Generation Sequencing

Noah Hoffman, M.D., Ph.D., Associate Professor, University of Washington, Department of Laboratory Medicine, Associate Director, Informatics Division, University of Washington Medical Center

Development of software tools for species-level classification of bacteria using next-generation sequencing, as well as processes for rapid and confident clinical sign out have been particularly challenging in the clinical laboratory setting. In this talk, I will present the development of one of the first NGS 16S gene sequencing assays to be offered by a clinical laboratory, discuss bioinformatic challenges and solutions, and present applications for this assay using case studies.

1:00 Session Break

1:15 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

2:15 Session Break

2:30 Chairperson’s Remarks

Weian Zhao, Ph.D., Assistant Professor, Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, University of California–Irvine

2:40 Large-Scale Whole Genome Sequencing in Microbiology

Stephen Salipante, M.D., Ph.D., Assistant Professor, Director, Next-Generation Sequencing Analytics Laboratory; Assistant Director, Molecular Diagnosis Section, University of Washington

Next-generation sequencing is making it increasingly feasible to generate whole genome sequence data from large numbers of microorganisms. This session will examine what kinds of information can be obtained from performing large-scale genomic sequencing of bacteria originating directly from the clinical laboratory.

3:10 Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories

Ira M. Lubin, Ph.D., FACMG, Branch Chief (acting); Team Lead, Genetics, Laboratory Research and Evaluation Branch, Division of Laboratory Systems/CSELS, Office of Public Health Scientific Services, Centers for Disease Control and Prevention

The Centers for Disease Control and Prevention published practice recommendations developed by multidisciplinary workgroups for clinical next-generation sequencing of human genomic DNA. To follow up, CDC began an effort to consider quality issues and guidance for NGS infectious disease testing. The similarities and differences applicable to NGS testing of human and infectious disease samples will be discussed.

3:40 Regulatory Perspective on Infectious Disease NGS Dx Devices

Heike Sichtig, Ph.D., Medical Countermeasures/Multiplex, Microbiology Devices, Center for Devices (CDRH), FDA

The presentation will outline studies to evaluate the use of NGS-based devices as an aid in infectious disease diagnostics, and to gain a better understanding of potential NGS clinical implementation strategies. Focus will be on the possible approaches to validation studies and data for the evaluation of infectious disease NGS-based diagnostics for potential regulatory clearance/approval, and the use of sequence outputs from infectious disease NGS-based devices to evaluate performance.

SeraCare(1)4:10 Clinical Testing Using an NGS-Based HIV-1 Genotyping Assay (DEEPGENTM HIV): The Importance of Utilizing a Stringent Quality Control

Miguel E. Quinones-Mateu, Ph.D., Associate Professor & Scientific Director, University Hospitals Case Medical Center/Case Western Reserve University

A robust validation and implementation process is essential to guarantee the success of NGS-based lab-developed tests (LDTs) in a CLIA-certified environment, including the use of appropriate controls, standards and reference materials. This presentation will describe the development and implementation of an ultrasensitive NGS HIV-1 genotyping assay (DEEPGENTM HIV) designed to detect minority drug-resistant HIV-1 variants and the use of novel recombinant RNA viral technology ‘full process’ reference material to monitor the detection of HIV-1 drug resistant targets.

4:25 Utility of Rapid Real-Time PCR using a Novel
Random-Access 20-Minute Real-Time PCR System

Christopher Connelly, Ph.D., Research and Development Scientific Manager, Molecular Technology, Streck

This talk will focus on PCR-based applications for the Philisa® Real-Time PCR System that serve to accelerate workflow for molecular diagnostic analysis. Critical assays for infectious disease testing, such as detection of antibiotic resistant bacteria and RT-PCR-based identification of viruses will benefit from the versatility and performance of the Philisa Real-Time PCR System.

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, March 8

7:00 am Registration Open and Morning Coffee

8:00 Plenary Keynote Session (see page 5 for details)

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


10:05 Chairperson’s Remarks

P. Mickey Williams, Ph.D., Director, Molecular Characterization & Clinical Assay Development Laboratory (MoCha), Frederick National Laboratory for Cancer Research

10:15 Preparing a Multi-Analyte NGS Assay for Use in Clinical Studies for Cancer

P. Mickey Williams, Ph.D., Director, Molecular Characterization & Clinical Assay Development Laboratory (MoCha), Frederick National Laboratory for Cancer Research

NGS offers a powerful tool for assessment of molecular defects found in cancer. The utilization of NGS is becoming common practice in clinical laboratories. This complex technology requires a new level of analytical performance testing and validation. This discussion will focus on approaches used for analytical validation of the NGS clinical assay used for treatment selection in the NCI-MPACT study. 

10:45 Setting Up a Large Sequencing Center: Assay Development Considerations

William Biggs, Ph.D., Head, Sequencing Operations, Human Longevity, Inc.

The desire to access valuable clinical FFPE samples using advanced molecular techniques such as next-generation sequencing methods in an efficient and productive manner represents an ongoing challenge for most clinical laboratories. At the Clinical Research Sequencing Platform (CRSP) within the Broad Institute methods have been developed, optimized and implemented which allow for the ready and routine access of FFPE samples for such NGS-based analyses as Whole Exome Sequencing and Targeted Re-Sequencing.

11:15 Development of a Clinical Cell-Free Circulating Tumor DNA Assay for Cancer Molecular Profiling

Geoff Otto, Ph.D., Senior Director, Molecular Biology & Sequencing, Foundation Medicine

Profiling circulating tumor DNA (ctDNA) for the genomic alterations (GA) driving oncogenesis promises to provide insight into cancer biology, inform therapy selection when conventional biopsies are unobtainable and enable monitoring of response to therapy. A clinical, NGS-based ctDNA assay was developed; highly accurate detection of GA was analytically validated; and clinical utility investigated from patient-matched FFPE and blood samples across lung, breast and colon cancer at different disease stages.

11:45 Approaches to High Efficiency Nucleic Acid Extraction and Purification from Diverse Sample Types for NGS-Based Pathogen Detection

David R. Hillyard, M.D., Professor, Pathology, University of Utah; Director, Molecular Infectious Disease Testing, Arup Laboratories

Rapid and efficient preparation of well-purified nucleic acids from diverse sample types has increasingly become a critical component of diagnostic testing. Applications such as infectious disease and circulating cell free genetic testing also demand great test sensitivity and may require extraction from larger sample volumes. This presentation will review both currently available and emerging approaches to nucleic acid extraction, and issues relevant to its integration with downstream amplification and analysis technologies for highly multiplexed targeted and NGS-based pathogen detection.

12:15 pm Session Break

NanoString212:25 Luncheon Presentation to be Announced I: Integrated Workflow and Sample Preparation for 3D BiologyTM: Simultaneous, Multiplexed Analysis of DNA, RNA, and Proteins

Joseph M. Beechem, Ph.D., Senior Vice President, Research & Development, NanoString Technologies

The field of 3D Biology—the ability to simultaneously quantify DNA (SNVs), mRNA, and proteins (including PTMs)—has been uniquely enabled through the use of NanoString’s molecular barcoding technology. Accomplishing this analysis requires integration of sample preparation, analytical instrumentation, and data analysis software. This presentation will describe the development of reagents and workflow designed to prepare specimens for 3D biology analysis on an nCounter® system. This low-sample-input method utilizes magnetic bead capture of cells, followed by automated DNA, RNA, and Protein counting.

Silicon Biosystems12:55 Luncheon Presentation II: DEPArray Digital Sorting of 100% Pure Tumor Cells Enables High Precision NGS on Low Input & Low Cellularity FFPE Samples

Farideh Bischoff, Ph.D., Executive Director, Scientific Affairs & Head of Clinical Development, Silicon Biosystems

NGS analysis of 100% pure cell populations sorted by DEPArray™ technology from FFPE samples provides unprecedented precision in describing the complete genetic of a tumor, including somatic variants, CNV, LoH, introducing a new way for precise stratification of patients.

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

Balancing Costs with Results and Regulatory Requirements

2:00 Chairperson’s Remarks

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

2:10 The Utility of Exome Sequencing in Providing Deep Coverage of Disease-Relevant Targets

Avni B. Santani, Ph.D., Assistant Professor, Clinical Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia

To date, disease-targeted gene panels have generated a lot of interest but exome sequencing (ES) is increasingly gaining acceptance for inherited and somatic diseases with locus and allelic heterogeneity. In this talk, we cover our group’s effort in creating a technically enhanced ES assay that provides adequate coverage of all currently known disease-relevant genes, thereby facilitating high quality exome interpretation as well as exome “slices” for disease panels. Key considerations for test optimization including cost, specimen pooling, data quality and compliance will be discussed.

2:40 Diagnostic Gene Panels in the Exome Era – Using Exome Sequencing as a Universal Assay to Streamline Assay Development and Laboratory Operations

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 accelerating pace of disease gene discovery is presenting an increasing challenge for diagnostic laboratories as updating targeted gene panels is costly. Improved exome sequencing assays achieve near equal quality and decreasing costs open the door to replacing gene panel assays with virtual panels. This presentation summarizes our experience moving from targeted gene panels to exome-based virtual panels using inherited renal disorders as an example.

3:10 Laboratory Accreditation and Proficiency Testing for Next-Generation Sequencing Diagnostics: An Update on College of American Pathologists Programs

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

By late 2015, nearly 200 laboratories accredited by the College of American Pathologists indicated that they offered next-generation sequencing-based diagnostics. This number is expected to grow. This presentation will provide an update on accreditation requirements developed by the College specific to laboratories performing NGS based diagnostics. 2015 also marked the launch of the College’s first methods-based proficiency testing program for NGS-based detection of germline variants, for which summary results will be discussed.

3:40 Genome-Wide Prenatal Cell Free DNA Testing: Validation and Clinical Experience

Daniel S. Grosu, M.D., MBA, CMO, Sequenom, Inc.

A significant proportion of chromosomal and subchromosomal abnormalities in the prenatal setting are not detectable by conventional cfDNA testing. Sequenom seeks to bridge this informational gap through a genome-wide approach that reports on whole chromosome aneuoploidies and CNVs  ≥7 Mb in size across the entire genome, in addition to select microdeletions <7 Mb in size. Validation and clinical experience data will be presented for the new approach.

3:55 Sponsored Presentation (Opportunity Available)

4:10 St. Patrick’s Day 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


Recent FDA Feedback, Tips and Trends for IVDs

Gail Radcliffe, President, Consulting, Radcliffe Consulting, Inc.


  • RTA Checklist: tips for jumping over the first hurdle
  • Next-Gen Testing: regulation snafu
  • CLIA Waiver: simple and low risk of erroneous result
  • De Novo: providing rationale to support De Novo classification


Improving the User Experience of Personalized Medicine

Piraye Y. Beim, Ph.D., Founder & CEO, Celmatix, Inc.


  • The role of digital tools in clinical decision support
  • The rise of the tech/biotech hybrid company, what biotech can learn from tech
  • Thinking about end users: what matters most to doctors versus patients
  • Regulatory challenges to changing how doctors and patients access genetic information


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


Rapid Detection Methods for Infectious Diseases

Weian Zhao, PhD, Assistant Professor, Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Biomedical Engineering, University of California, Irvine


  • What do you think are the biggest problems remaining in the field?
  • How do the rapid infectious disease test and monitoring fit into the new digital health paradigm?
  • Discussions on rapid test of antibiotic resistance and precision medicine


6:00 Close of Day

Wednesday, March 9

7:00 am Registration Open

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

8:00 Plenary Keynote Session Panel

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


10:50 Chairperson’s Remarks

Carl Wittwer, M.D., Ph.D., Professor, Department of Pathology, University of Utah

11:00 BRACAnalysis CDx: First Laboratory Developed Companion Diagnostic Approval Story

Jolette Franco, Director, Regulatory Affairs, Myriad Genetic Laboratories, Inc.

Short presentation on the PMA approval journey of a laboratory developed companion diagnostic test in conjunction with the approval of AstraZeneca’s drug Lynparza.

11:15 One Assay, Two Guvnors: Development of FDA-Approved PCR for the Clinic

Adrian Moody, Ph.D., Director & Head, Design and Development Manchester, MDx Assay Development, QIAGEN

QIAGEN’s leadership in companion diagnostics continues to grow, transforming patient care around the world. Our therascreen EGFR test is driving treatment decisions in lung cancer patients across the globe and will be used as a case study to explore the challenges of developing FDA approved PCR in the clinic.

11:30 PANEL DISCUSSION: FDA Approval of PCR- and NGS-Based Diagnostics

Moderator: Carl Wittwer, M.D., Ph.D., Professor, Department of Pathology, University of Utah

Panelists: Jolette Franco, Director, Regulatory Affairs, Myriad Genetic Laboratories, Inc.

Adrian Moody Ph.D., Director, Head, Design and Development Manchester, MDx Assay Development, QIAGEN

This discussion will cover:

  • Reimbursement
  • Logistical considerations
  • Value perception
  • Test evidence evaluation

12:30 pm 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

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

2:00 Novel Clinical Applications of Cancer Genomics

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

Novel technologies to evaluate genomics-based tumor burden in tumor tissue and bodily fluids 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.

2:30 What is a Cancer Mutation? Challenges in Detecting, Interpreting, and Targeting Somatic Variants

Joshua M. Stuart, Ph.D., Baskin Engineering Endowed Chair & Professor, Biomolecular Engineering,; Associate Director, Center for Biomolecular Science and Engineering, University of California, Santa Cruz

DNA sequencing provides an unprecedented potential to catalog all somatic alterations in tumor genomes. Yet the task of assembling raw reads into biologically-interpretable information is still a “Wild West” of algorithms. In the talk, I will discuss an open competition to identify the best mutation calling algorithms. After a year of collecting results from hundreds of methods, we learned some ingenious tricks from some, and pitfalls that tripped up most, competitors.

3:00 Noninvasive Monitoring of Lymphoma by Sequencing of Circulating Tumor DNA

Ash A. Alizadeh, Ph.D., Principal Investigator, Assistant Professor, Medicine, Divisions of Oncology & of Hematology; Attending Physician, Lymphoma Oncology Clinic, Stanford Cancer Center, Stanford University

Recent studies have shown limited utility of routine surveillance imaging for diffuse large B-cell lymphoma (DLBCL) patients achieving remission. Detection of molecular disease in peripheral blood provides an alternate strategy for surveillance. I will describe strategies for noninvasive monitoring of lymphoma by sequencing of circulating tumor DNA, including performance characteristics of various assays, their clinical applications, and their promise for future translations studies.

3:30 NGS-Based Diagnostics: Developing Assays and Monitoring Performance Using Novel Biosynthetic QC Tools

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

Results from an Inter-Laboratory Study Using Novel Biosynthetic QC Tools: There are currently no widely-accepted NGS QC standards for multi-analyte diagnostic assays which hampers the ability to compare the performance of different assays. Preliminary results will be presented from a study testing the SeraseqTM Solid Tumor Mix-I as a qualitative and quantitative QC indicator for tumor profiling.

4:00 Session Break

4:10 Chairperson’s Remarks

German Pihan, M.D., Staff Pathologist and Director, Diagnostic Hematopathology Service, Pathology, Beth Israel Deaconess Medical Center

4:15 Darwinian Cancer Genome Evolution: The Achilles Heel of Precision Cancer Medicine. Can It Be Overcome?

German Pihan, M.D., Staff Pathologist and Director, Diagnostic Hematopathology Service, Pathology, Beth Israel Deaconess Medical Center

The high rate of mutations in cancer is the single most important challenge to the success of precision medicine in cancer. Whole genome sequencing is beginning to elucidate the patterns, pathways and causes of the astonishingly dynamic high rate of somatic mutation in most cancers. Understanding these pathways will prove challenging but fundamentally important to succeed in the fight against cancer. This talk will define the nature of the Darwinian cancer genome evolution challenge and propose possible avenues to surmount it.

4:45 Who Should Regulate Cancer NGS Tests: FDA, CMS/CLIA, or Both?

Roger D. Klein, M.D., J.D., Chair, Professional Relations Committee, Association for Molecular Pathology (AMP); Medical Director, Molecular Oncology, Cleveland Clinic

This presentation will discuss current controversies and potential regulatory approached for the oversight of next generation sequencing testing for oncology applications.


5:45 Close of Conference Program