Cambridge Healthtech Institute’s Third Annual

Genomics in Medicine

Data-Driven Personalized Diagnostics for Improved Outcomes

February 19-20, 2015 | Moscone North Convention Center | San Francisco, CA
Part of the 22nd International Molecular Medicine Tri-Conference


The rapid decline in cost and widespread utilization of patient genomic information is now dramatically impacting clinical research—offering significant benefits to patients, clinicians, researchers and developers working to accurately diagnose pathologies and deliver personalized treatments. The Genomics in Medicine symposium will once again gather stakeholders to discuss advances highlighting the impact and clinical utility of patient sequencing; integration of genomics data into medical practice; identification, annotation and interpretation of variants; as well as sharing and mining data to guide treatment.

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Thursday, February 19

7:30 am Registration and Morning Coffee


9:00 Chairperson’s Opening Remarks

Robert Penny, M.D., Ph.D., CEO, Paradigm


Update on the MedSeq and BabySeq Projects: Randomized Trials of Sequencing in Adults and Newborns

Robert C. Green, M.D., MPH, Director, G2P Research Program; Associate Director, Research, Partners Center for Personalized Genetic Medicine, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School

This talk will present new data from the NIH-funded MedSeq and BabySeq Projects, two of the first randomized trials of genome sequencing versus standard of care, currently being conducted in adults and newborns, respectively. These projects explore the impact of integrating genome sequencing with the practice of medicine in both sick and healthy individuals, measuring medical, behavioral and economic outcomes for patients; and exploring the experience of non-geneticist physicians confronting genomic data in their patients.

9:40 The Vision and the Reality: One Cancer Center’s Journey toward Genomic Medicine

Jeff Boyd, Ph.D., Senior Vice President, Molecular Medicine; The Robert C. Young Chair in Cancer Research; Executive Director, Cancer Genome Institute; Chief, Division of Molecular Pathology; Professor, Cancer Biology Program, Fox Chase Cancer Center

10:10 The Impact of Genomic Variation in Clinical Development

Hakon Hakonarson, M.D., Ph.D., Director, Center for Applied Genomics, Children’s Hospital of Philadelphia

This presentation will focus on genomic strategies applied in academia to enrich for genetic variants that may inform drug discovery and development for complex medical disorders affecting both children and adults.

10:40 Coffee Break with Exhibit and Poster Viewing


11:15 Integration of Genetics and Genomics into Medical Practice: Educational Challenges

Bruce R. Korf, M.D., Ph.D., Wayne H. and Sara Crews Finley Chair in Medical Genetics; Professor and Chair,Genetics; Director, Heflin Center for Genomic Sciences, University of Alabama at Birmingham

Genetics and genomics offers major opportunities to improve health and increase the power of diagnosis and treatment of disease across all areas of medicine. Most physicians in practice today were trained prior to the genomics era, and even students currently in training have limited exposure to this new area of medicine. Taking full advantage of the genetic and genomic approach will require changes in health professional education, including achieving basic competencies in genetics and genomics and having a specialty genetic and genomic workforce to provide assistance.

11:45 Navigating the Genome: Realizing the True Promise of Genomic Medicine in the Clinic

James Evans, M.D., Ph.D., Bryson Distinguished Professor, Genetics and Medicine,Genetics, University of North Carolina School of Medicine

Great advances have been made in our ability to analyze the genome.However, not all basic science advances yield clinical benefit. Where can our new revolutionary sequencing technologies actually benefit human health in the short term?

12:15 pm Paradigm Cancer Diagnostic (PCDx): Development of a Clinical-Grade Next-Generation Sequencing Test for Cancer Patients

Robert Penny, M.D., Ph.D., CEO, Paradigm

Paradigm is an emerging molecular information organization, delivering precision medicine to cancer patients. Incorporating learning’s from TCGA and other diagnostic efforts, Paradigm has developed a clinical-grade test to interrogate key alterations in the cancer genome including mRNA, DNA mutations, fusions.

12:30 Session Break

12:40 Luncheon Presentation: Enabling Translational Diagnostics through Discovery and Development of Signatures with Unified DNA and RNA NGS Panels 

Brian Haynes, Ph.D., Senior Scientist, Asuragen

We present a comprehensive solution for NGS-based biomarker discovery and the translation of these markers to our targeted NGS assay, SuraSeq®, using poor quality and low-quantity (FFPE or FNA) tumor biopsies. SuraSeq® enables the simultaneous interrogation of DNA and RNA from total nucleic acid and provides detection and quantification of DNA mutations, expression markers, and RNA fusions to advance diagnostic, prognostic and theranostic applications, clinical trial assays, and in vitro diagnostic products.

1:15 Session Break


1:50 Chairperson’s Remarks

James Evans, M.D., Ph.D., Bryson Distinguished Professor, Genetics and Medicine, Genetics, University of North Carolina School of Medicine

2:00 PANEL DISCUSSION: Practical Considerations for Integration of Genomic Data in Medical Practice

While NGS technologies continue to usher in a new era of genomic medicine, many practical considerations and issues have emerged. These include: the return of patient information; reimbursement of genomic tests; reporting results to physicians, and the sequencing of healthy newborns. This panel will provide an open format for stakeholders to address these issues, while shedding light on best practices.


James Evans, M.D., Ph.D., Bryson Distinguished Professor, Genetics and Medicine,Genetics, University of North Carolina School of Medicine

3:00 Refreshment Break with Exhibit and Poster Viewing


3:30 Genomic Approaches to Causal Variant Identification

Gregory Cooper, Ph.D., Faculty Investigator, HudsonAlpha Institute for Biotechnology

Sequencing technologies now routinely provide comprehensive maps of genetic variation in individual human genomes, but analytical challenges slow progress in the precise and robust identification of those genetic variants that are causally relevant to human phenotypes. Variants outside of protein-coding exons are particularly difficult to evaluate. I will discuss ongoing work to develop variant annotations to improve both coding and non-coding causal variant identification. I will also discuss results from use of those annotations in both clinical and research sequencing projects, in particular for the identification of variants that are diagnostically relevant to intellectual disability and developmental delay.

4:00 Decoding the Patient’s Genome: Clinical Use of Genome-Wide Sequencing Data

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

Despite significant advances in our understanding of the genetic basis of disease, genome-wide identification and subsequent interpretation of the molecular changes that lead to human disease represent the most significant challenges in modern human genetics. Starting in 2009 at MCW, we have performed clinical WGS and WES to diagnose patients coming from across all clinical specialties. I will discuss findings, pros and cons in approach, challenges remaining and where we go next.

4:30 Clinical Grade Annotations: Public Data Resources for Interpreting Genomic Variants

Gabe Rudy, Vice President, Product Development, Golden Helix

NGS is providing affordable and data-rich assays for rare disease diagnosis, carrier screening, risk prediction, pharmacogenomics and oncology care. But the public sharing of clinically relevant annotations is not even across these applications. In this talk, I review the fundamental mechanics and challenges of annotating NGS data for clinical grade reporting and interpretations. I compare the accessibility of dbSNP, OMIM, ClinVar, HDMD and COSMIC and how these repositories of clinically relevant annotations are accessed and applied to the interpretation process.

5:00 Close of Day

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Friday, February 20

8:00 am Morning Coffee


8:25 Chairperson’s Remarks

Brian Haynes, Ph.D., Senior Scientist, Asuragen

8:30 Rapid Genome Sequencing, Interpretation and Management in the Neonatal Intensive Care Unit

Euan Ashley, D.Phil., Associate Professor, Medicine and Genetics; Director, Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine

Genetic testing in patients with malignant cardiac arrhythmias can focus personalized management on the underlying cause. In the neonatal setting, the ability to rapidly identify the underlying cause of a malignant arrhythmia can be potentially lifesaving. In this talk, I will outline recent approaches to rapid genome sequencing and interpretation at Stanford hospital and clinics and give examples from patients admitted to the neonatal intensive care unit at Lucile Packard Children’s Hospital.

9:00 Reinterpreting Results from Large-Scale Clinical Sequencing or Genetic Testing

Peter Byers, M.D., Director, Center for Precision Diagnostics; Professor, Pathology, Medicine & Genome Sciences, University of Washington School of Medicine

9:30 The Clinical Ramifications of Divergent Oncogenic Pathways in Tumor Evolution

Hanlee Ji, M.D., Assistant Professor,Oncology, Medicine, Stanford University School of Medicine; Senior Associate Director, Stanford Genome Technology Center

Tumor evolution and the resulting clonal diversity is a common process that affects nearly all malignancies and has significant ramifications for precision cancer medicine. Namely, the use of targeted therapies is significantly complicated by the genetic variance that is a part of tumor evolution. To understand this process requires innovative methods of discriminating the divergent oncogenic pathways that are in play as part of clonal diversity and evolution. New molecular and computational approaches will be described that address this fundamental issue of developing genomic-oriented cancer

10:00 Sponsored Presentations (Opportunities Available)

10:30 Coffee Break with Exhibit and Poster Viewing


11:00 Impact & Utilization of Integrating Genomic Data into EMRs

Dan Roden, M.D., William Stokes Professor, Experimental Therapeutics; Professor, Medicine and Pharmacology; Assistant Vice Chancellor, Personalized Medicine, Vanderbilt University

11:30 Mining Clinical Genomic Data

Joel Dudley, Ph.D., Director, Biomedical Informatics; Assistant Professor, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

12:00 pm The ClinGen Resource: Sharing Data. Building Knowledge. Improving Care.

Christa Lese Martin, Ph.D., FACMG, Director & Senior Investigator, Autism & Developmental Medicine Institute (ADMI), Geisinger Health System

Technological advances are quickly allowing genome-wide analysis to become commonplace in the care of patients. However, the ability to detect DNA variants has greatly surpassed the ability to interpret their clinical impact, limiting patient benefit. Improving genomic interpretation will require a coordinated effort from both the clinical and research communities. The Clinical Genome Resource (ClinGen) is a collaborative National Institutes of Health (NIH)-funded program dedicated to harnessing the data from both research efforts and clinical genetic testing, and using it to propel expert and machine-driven curation activities. By facilitating collaboration within the genomics community, we will build our collective knowledge base, moving closer to the promise of personalized genomic medicine.

12:30 Close of Symposium

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