2013 Archived Content

Clinical Sequencing

Translating NGS from Research to Practice


Day 1 | Day 2 | Day 3 

Thursday, February 14

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

8:00 - 9:40 Plenary Keynote Panel: Emerging Technologies & Industry PerspectivesThis session features a series of presentations on emerging and hot technologies in diagnostics, drug discovery & development, informatics, and oncology. Interactive Q&A discussion with the audience will be included. - Read more 

Sponsored by



Biocartis  Elsevier  Luminex  RemedyMD  Scientia Advisors  Singulex 


9:40 Refreshment Break in the Exhibit Hall with Poster Viewing


NGS Diagnostics onto the iPad: Understanding
the Physician Workflow

10:40 Chairperson's Remarks

Alan Carter, Chief Business Officer, PanGenX

10:45 The Clinical Utility of T2DM and Other Genetic Risk Testing in Primary Care?

Alex Cho, M.D., MBA, Assistant Professor, Department of Medicine, General Internal Medicine, DUHS Center for Personalized Medicine, Duke University

Primary care spans the full spectrum of healthcare: preventive care for those who are currently healthy; risk management for those who have preclinical disease; and diagnosis, prognosis, and treatment for those with active disease.  Genomics can be employed by providers at each step in the progression from health to advanced disease, providing information regarding disease risk or susceptibility; as well as response to pharmacotherapy, including side effects.  The mechanisms by which such information can aid providers can be sorted into four categories:  tailoring prevention strategies; raising provider awareness (for certain disease possibilities); selecting optimal therapy; and encouraging patient engagement.  Through specific use cases relevant to primary care, the potential utility, limitations, and practical challenges to employing genomics in this manner will be explored.

11:15 Decision Support for Personalized Genomic Medicine

Mark S. Boguski, Ph.D., Associate Professor, Center for Biomedical Informatics, Harvard Medical School

11:45 Turn-Key and Precise Clinical Genome Interpretation

Dietrich Stephan, Ph.D., Founder & CEO, Silicon Valley Biosystems (SVBio)

Genomes are beginning to make their way into the practice of medicine. Clinical diagnostics requires a level of accuracy and simplicity that is far different from the research uses of genomic data. We provide a turn-key service to interpret the human genome to improve patient outcomes in several clinical areas.

Luminex12:15 pm Luncheon Presentation I: Multiplexed Molecular Testing for Rapid Diagnosis of Gastrointestinal Infections

Kimberle C. Chapin, M.D., Lifespan Academic Medical Centers and Brown Medical SchoolA discussion on the evaluation of a multiplex molecular test to rapidly identify the top pathogens involved in gastroenteritis and its potential impacts across the various hospital care continuum.

Sunquest 12:45 Luncheon Presentation II: Inspection Ready - Regulatory Compliance of LDTs in Accredited Clinical Laboratories Can Be Eased By Utilizing the LISMegan Schmidt, Product Manager, Sunquest Information Systems
Clinical laboratories are subject to robust oversight by federal, state and professional entities. LDTs are subject to special scrutiny. Attendees will learn how the LIS can support a quality system with protocol adherence, checklist activities and quality assurance for confident inspection readiness. 

1:15 Refreshment Break in the Exhibit Hall with Poster Viewing


Real Data and Practical Challenges in Implementing Ngs 

1:40 Chairperson's Remarks

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

1:45 Computational Programs and Algorithms (Software) for Exome Sequence Analysis

Gaddy Getz, Ph.D., Director, Cancer Genome Computational Analysis, Broad Institute

2:15 Bioinformatics Challenges for Clinical Genome Sequencing

Stuart Brown, Ph.D., Professor of Bioinformatics, New York University

There are two major classes of challenges that must be overcome in order to apply genome sequencing to clincial diagnositcs. First is establishing the accuracy of the data. Each type of DNA sequencing machine has its own error profile which can be influenced by biosample preparation methods, target selection, chemistry of sequencing reagents, and software used for base calling and variant detection. We are exploring the relationship of coverage depth to false variant predictions with respect to different Exome enrichment kits. Second is the functional interpretation of mutation data. A large body of data is becoming available for allele frequencies of a comprehensive genome-wide set of mutations across healthy and diseased populations, somatic mutations etc. New data from the ENCODE project provides additional functional information about the regulatory potential of non-coding mutants. Our ability to build causal predictive models for genome sequences that integrate all of these factors will improve with access to large numbers of human genome sequences coupled with phenotype information.

2:45 Recent Insights from Next-Generation Sequencing (NGS) of Advanced Prostate Cancer

Akash Kumar, B.Chem.E, M.S., M.D./Ph.D. Candidate, Genome Sciences, University of Washington

This talk will discuss the results of a recent exome sequencing survey of lethal prostate cancers. I also intend to discuss some potential challenges associated with the introduction of NGS into oncology, including standardization of library preparation and intra-patient genomic heterogeneity.

Feeney Law Group3:15 What Everyone Working in the Life Sciences Needs to Know About AIA and the Recent SCOTUS/Federal Circuit DecisionsAlan F. Feeney, Esq., Owner, Feeney Law GroupThere have been several recent important developments effecting the patenting of life science discoveries. The America Invents Act and recent SCOTUS decision in validating patents directed to drug dosing have changed the standard for patenting biological discoveries. In 2013, SCOTUS will address the patentability of genes. Best patent practices, clever licensing strategies and effective prior art searches will be discussed.

Telome Health3:30 TeloTest™: A Transformative Telomere Length Assay in Personalized Medicine for Health Monitoring and Disease InterceptionCalvin B. Harley, Ph.D., CSO, Telome Health, Inc.Short telomeres at chromosome ends signal aging, loss of regenerative capacity, and increased disease and mortality risk. TeloTest™ is an accurate, high throughput, non-invasive qPCR assay to monitor telomere length in saliva, and improve health, and healthspan, by early intervention.

3:45 Valentine's Day Celebration and Poster Competition Winner Announced in the Exhibit Hall (Last Chance for Poster Viewing)


Case Studies in Implementation of Genomic Medicine 

4:30 Chairperson's Remarks

Mark S. Boguski, Ph.D., Associate Professor, Center for Biomedical Informatics, Harvard Medical School

4:35 Genomics and the Personalization of Ovarian Cancer Care

David Huntsman, M.D., FRCPC, FCCMG, Medical Director, Center for Translational & Applied Genomics, British Columbia Cancer Agency

Genomics and the personalization of ovarian cancer care: The approach to ovarian cancer care is changing from generically applied platinum/taxane based regimens to a stratified approach that recognizes the biologic and clinical distinctions between the common histologically defined subtypes. Genomic studies have both added credence to the concept that these subtypes are separate diseases and provided opportunities to further personalize care based on targetable genomic features. As is the case with many cancer the potential impact of intratumoral heterogeneity on diagnostic approaches, treatment decisions and responses to therapy are being studied but are not yet defined. In addition to being used to select treatment options the mutation profiles of ovarian cancer can readily be used to develop patient specific monitoring tools.

5:05 Making a Definitive Diagnosis: Opportunities and Challenges Associated with Clinical Application of Whole Genome Sequencing

Elizabeth Worthey, Ph.D., Assistant Professor, Pediatrics & Bioinformatics Program, Human & Molecular Genetics Center, Medical College of Wisconsin

We recently completed a pilot program aimed at developing a clinically appropriate system for WGS MDx. We defined processes for case selection, education, consent, analysis, data return, and reporting. A permanent WGS based clinic is now in place. I will discuss the types of opportunities and challenges associated with each aspect of this process, and will review details from specific cases.

5:35 Case Study in Autism

Timothy W. Yu, M.D., Ph.D., Instructor in Pediatrics, Children’s Hospital Boston and Department of Neurology, Lurie Center for Autism, Mass General Hospital for Children

6:05 Sponsored Presentations (Opportunities Available)

6:35 Close of Day

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