Next generation sequencing (NGS) has revolutionized genomics and is now on the verge of being widely adopted for medical sequencing. Whole exome or whole genome sequencing (WES/WGS) is the ultimate genetic test and many success stories provide a taste of its power. Targeted NGS based gene panels are typically an order of magnitude smaller than WES/WGS based testing but follow the same principles. However, while the cost of generating high-quality whole genome sequence data is rapidly dropping, analysis of the enormous number of variants detected is still very complex, and a task of annotating NGS data for clinical grade reporting and interpretations remain a challenge. Cambridge Healthtech Institute’s Inaugural NGS Diagnostics: Data Considerations, Annotation and Interpretation conference is designed to discuss best practices in NGS data analysis and results annotation. Some novel applications of NGS including pathogen detection and cell free DNA sequencing and RNA sequencing will be discussed as well.

WEDNESDAY, AUGUST 19

10:30 am Registration

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

TACKLING INTERPRETATION AND ANNOTATION CHALLENGES

1:50 Chairperson’s Opening Remarks

Wayne W. Grody, M.D., Ph.D., UCLA School of Medicine

2:00 Annotation and Interpretation of Clinical Exome Sequencing

Wayne W. Grody, M.D., Ph.D., Professor, Medical Genetics and Molecular Pathology, Pathology & Lab Medicine, Pediatrics, and Human Genetics; Director, Molecular Diagnostic Laboratories and Clinical Genomics Center, UCLA School of Medicine

Our center has been performing clinical-grade whole-exome sequencing (WES) for the diagnosis of rare Mendelian disorders since January 2012. In addition to our in-house bioinformatics pipeline and externally available databases and algorithms, all mutations and variants are interpreted by a unique “Clinical Genomics Board” comprised of lab directors, technologists, bioinformaticists, genetic counselors, medical geneticists, and the ordering clinicians. We find that this approach provides the most “value-added” clinical insight for proper annotation and reporting of variants. As a result, definitive pathogenic variants were identified and reported in 27% of all cases, and likely pathogenic variants were detected in an additional 28%, producing an aggregate diagnostic yield of up to 55%.

2:30 Precision Medicine – Challenges Associated with Annotation and Interpretation of Somatic Mutation Data

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

The past several years have seen a significant increase in the demand for somatic mutation testing in human cancers in order to specifically tailor therapeutic management strategies to specific patients. Many laboratories have begun testing for various numbers of mutations in large numbers of genes using massively parallel sequencing to provide genomic profiles that would direct therapeutic selection. This lecture will discuss the challenges associated with data analysis from the perspective of annotation and interpretation for routine clinical practice.

3:00 Interpretation of Exome Sequencing: Opening the Floodgates

Karen Weck, M.D., Professor of Pathology & Laboratory Medicine and Genetics, University of North Carolina, Chapel Hill

Massively parallel sequencing is an attractive modality for the diagnosis of genetic disorders. However, a major challenge with implementation in the clinical setting is interpretation of the huge numbers of genomic variants identified in an individual patient. The NCGENES (North Carolina Clinical Genomic Evaluation by Next-generation Exome Sequencing) project is evaluating the use of whole exome sequencing (WES) as a diagnostic tool in patients with a variety of suspected genetic conditions. We have established a priori diagnostic gene lists tailored to clinical phenotypes in order to streamline interpretation of genomic variants and increase the positive predictive value of WES. In this talk, I will define several categories of “uncertain” results that may be generated by WES and discuss strategies employed to adjudicate WES results. Defining the pathogenicity of individual variants is important, but it is also necessary to consider the phenotype to assess the overall diagnostic yield of such testing. Results of sequencing >400 patients indicate that diagnostic yield of WES is strongly influenced by the clinical indication for testing.

3:30 Sponsored Presentation (Opportunity Available)

4:00 Refreshment Break in the Exhibit Hall with Poster Viewing

CHALLENGES AND PROSPECTS AHEAD FOR LDTS

4:45 REGULATORY PANEL:

Moderator: Andrew C. Fish, Executive Director, AdvaMedDx

This session will review current issues related to FDA oversight of laboratory developed tests (LDTs) and offer perspectives from key stakeholders, including regulators, laboratories, manufacturers, and clinicians. The panel will discuss topics including the status and content of FDA proposed guidance on LDT oversight, any legislative and policy updates, evidence expectations regarding analytical and clinical validity, and compliance challenges.

Panelists:

Katherine Serrano, Ph.D., Biomedical Engineer, Chemistry & Toxicology Devices, FDA CDRH

Elissa Passiment, Executive Vice President, American Society for Clinical Laboratory Science (ASCLS)

Roger D. Klein, M.D., J.D., Pathologist, Molecular Pathology, Cleveland Clinic Foundation

Richard L. Schilsky, M.D., FACP, FASCO, CMO, American Society of Clinical Oncology

6:15 Close of Day

6:00 Dinner Short Course Registration

THURSDAY, AUGUST 20

ACCESS AND VALUE OF NGS DATA: DRIVING CLINICAL DECISION MAKING ACROSS DISEASE AREAS

8:25 Chairperson’s Opening Remarks

Harry Glorikian, Healthcare Consultant

8:30 A New Business Model in Laboratory Testing – Sharing Data

Carl Morrison, M.D., DVM, Executive Director, Center for Personalized Medicine; Director, Roswell Park Cancer Institute

Prior models of revenue streams for laboratories have been almost exclusively from 3rd party payers for laboratory services provided. As laboratories move from traditional single analyte testing to comprehensive multi-analyte platforms the ability to generate 2nd and 3rd uses of this data has the ability to generate additional revenue streams. Dr. Morrison will present how his group is using this new business model to achieve new avenues of commercialization for laboratory testing through the OmniSeq program.

8:45 NGS: Filling in the Gaps

Erynn Gordon, MS, LCGC, Medical Marketing Director, 23andMe

The use of Sanger sequencing and array based testing over the past few decades has made genetic testing available to patients with clear Mendelian disorders. However, the cost and time involved has been a burden to patients and many have been left without answers. NGS has shifted the genetic testing paradigm allowing many, if not all, genes to be queried at once.

9:00 New Knowledge from NGS and Big Data

Felix W. Frueh, Ph.D., Executive Partner, Opus Three LLC

The ability to integrate NGS in larger contexts of diverse health care data provides the opportunity to interpret the human genome at increased precision. Such interpretation creates the foundation for new knowledge (e.g. associations between genome-level data and clinical manifestations) that will drive clinical decision making in molecular medicine.

9:15 Improve Cancer Treatments by Incorporating the NGS Data of Tumor Samples

Han Liang, Ph.D., Associate Professor and Deputy Chair, Bioinformatics and Computational Biology, R. Lee Clark Fellow, The University of Texas MD Anderson Cancer Center

An important task in cancer research is how to accurately identify biomarkers and use them to predict the prognosis or drug responses of cancer patients. Using the genomic data from large-patient cohorts, we evaluated the power of diverse types of molecular data in predicting patient survivals and annotated the functional effects of mutational hotspots in clinically actionable genes across tumor types.

9:30 Cross-Industry Partnerships to Foster Innovation and Decrease Manufacturing Time to Market in the Biomedical Business

Ali Tinazli, Ph.D., Vice President, Head, Business Development & Sales, Sony DADC Biosciences

Smart Consumables based on polymer materials with microscale or supreme optical features are prerequisites for emerging applications in the biomedical markets as in in vitro diagnostics. The increasing complexity of such new product, including CMOS hybrid consumables, requires new manufacturing technologies.

9:45 Sponsored Presentation (Opportunity Available)

10:00 Coffee Break in the Exhibit Hall with Poster Viewing

ACCESS AND VALUE OF NGS DATA

10:50 PANEL DISCUSSION:

Moderator: Harry Glorikian, Healthcare Consultant

• What are the value creation points for the data? How does the data make a difference in how someone is treated?
• Ensuring access to and organizing and managing data
• How are partnering deals structured? What are some key issues?
• How do you monetize the value of the data?
• Is the data more valuable than the technology that creates it?

Panelists:

Carl Morrison, M.D., DVM, Executive Director, Center for Personalized Medicine; Director, Roswell Park Cancer Institute

Erynn Gordon, MS, LCGC, Medical Marketing Director, 23andMe

Felix W. Frueh, Ph.D., Executive Partner, Opus Three LLC

Han Liang, Ph.D., Associate Professor and Deputy Chair, Bioinformatics and Computational Biology, R. Lee Clark Fellow, The University of Texas MD Anderson Cancer Center

12:20 pm Sponsored Presentation (Opportunity Available)

12:50 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:20 Session Break

NGS ANNOTATION IN GENOMICS, GENETICS, AND RNA-SEQ

2:00 Chairperson’s Remarks

Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity

2:05 The NGS Annotation Landscape for Genomics, Genetics, and RNA-Seq: Current Challenges for Commercial Clinical Labs

Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity

Advanced sequencing technologies are highly dependent on bioinformatics tools and appropriate interpretation. In addition to applying the optimized bioinformatic algorithms with specific, validated thresholds, transforming the data into clinically useful information requires appropriate annotation. The application typically dictates the knowledge base of choice as well as the clinical interpretation. Selecting or building the appropriate bioinformatics, annotation solutions and clinical interpretation are challenges for commercial clinical labs that will be discussed within the context of Genomics, Genetics, and RNA-Seq.

2:35 Joint Presentation: The VA Precision Oncology Program with N-of-One: Optimizing The Use of NGS Results to Enable a Partnership Between Clinical Care and Research

Louis Fiore, M.D., Executive Director, MAVERIC, Boston VA Healthcare System

Jennifer Levin Carter, M.D., CMO & Founder, N-of-One

The Department of Veterans Affairs New England Healthcare system has recently launched the Precision Oncology Program. The Program offers targeted sequencing to all patients with non-small cell lung cancer and returns annotated results to clinicians for clinical care decision making. A research agenda adds clinical trial matching and data repository creation as value-added components of the Program. This presentation will focus on the process of clinical interpretation of the NGS results by N-of-One and the clinical use of those interpretations in the VA.

3:05 Databases and Case Review: An In-House Developed Program for a Mid-Sized Academic Laboratory

Jennifer Morrissette, Ph.D., Scientific Director, Clinical Cytogenetics Laboratory, Clinical Director, Center for Personalized Diagnostics (CPD), University of Pennsylvania Perelman School of Medicine

Genomic technologies have revolutionized clinical landscape of oncology, with the ability to detect mutations in many genes at relatively low cost. As more targeted therapies are available, both as FDA cleared treatments and in the clinical trial setting, more clinicians are demanding genomic data on their patient’s tumors, looking for a therapy to exploit individualized for the mutations present in the tumor tissue. Laboratories are increasingly moving into next-generation sequencing (NGS) as the costs have decreased and the technologies have become more robust. There are many choices of how to process and analyze data coming off the machine, some sequencer-specific analysis tools, commercial entities and in-house solutions. This talk will describe a laboratory developed LIMS system, covering sample management, analysis and reporting developed for identification of abnormalities in DNA and RNA used in a clinical laboratory setting.

3:35 PANEL DISCUSSION: Annotation Whole Exome Sequencing and Panels: Practical Approaches

Moderator: Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity

• Data analysis approaches and challenges in next-generation sequencing
• User-friendly and accurate databases: do they exist?
• Handling the incidentalome
• New requirements for informed consent

4:05 Close of Conference