TCGC: Clinical Genome ConferenceTCGC: Clinical Genome ConferenceTCGC: Clinical Genome Conference

June 25-26, 2013

Bio-IT World & Cambridge Healthtech Institute’s Second Annual 

TCGC: The Science of Investigation
and Interpretation


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Tuesday, June 25

7:45 am Conference Registration and Morning Coffee

Opening Keynote Session 

8:30 Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

8:45 Integrating Genome Sequencing into Clinical Medicine: When, Why, and How?

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

The technology of genome sequencing is advancing much more rapidly than the knowledge of how to use the large volume of genomic information to achieve better prevention and management of disease. This talk will review some of the possible clinical applications of genome sequencing, the barriers to implementation, and some approaches that may help to overcome these barriers.

9:30 Delivering Genomic Medicine: Challenges and Opportunities

Heidi RehmHeidi L. Rehm, Ph.D., FACMG, Assistant Professor of Pathology, Brigham and Women’s Hospital and Harvard Medical School; Director, Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine

This talk will address our experience in offering genomic sequencing services, including data analysis and clinical interpretation and reporting. It will address innovative solutions to increase the efficiency of genomic reporting through software solutions and widespread data sharing.

PodcastClinical Genetics and Genomic Medicine with Heidi Rehm 

10:15 Morning Coffee Break

10:30 Progress in Aggregating All the World’s Genetic Tests into a Single Assay

Randy ScottRandy Scott, Ph.D., Chairman and CEO, InVitae

Rare genetic diseases have long suffered from a lack of research due to limited commercial interest. However, there are thousands of Mendelian inherited genetic disorders and millions of affected individuals worldwide. Our goal is to aggregate all of the world’s genetic tests into a single assay for less than the cost of a single gene assay today by applying the power of next-generation DNA sequencing and allowing routine testing for even rare conditions.

PodcastCreating a Clinical Genomics A-Team with Randy Scott 

11:15 Genetics of Common/Complex Clinical Problems

Kári StefánssonKári Stefánsson, M.D., Dr. Med., CEO, President, and Director, deCODE genetics


12:00 pm Close of Session

knome 12:15 Luncheon Presentation: Routine, Reliable Genomic Interpretation: A Call for a Fully Integrated System of Software and Reference Data

Ben SalisburyBen Salisbury, Ph.D., Vice President, Clinical Genomics, Knome, Inc.

By its nature, genome sequencing uncovers millions of variants ranging from clinically understood to novel and ambiguous. To address this variety, an analysis pipeline must accurately map each variant to common coordinates and tie it together with disparate external sources of information and predictive assessments. Institutional knowledge must also be incorporated. In a clinical context, this process must be reliable, repeatable, controlled, and readily validated. A solution that satisfies many of these needs will be presented.

Sample Collection 

1:45 Chairperson’s Remarks

Catherine A. Brownstein, Ph.D., MPH, Gene Partnership, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School

1:50 EngageUC: Advancing Biorepository Research at the University of California

Daniel DohanDaniel Dohan, Ph.D., Associate Professor & Associate Director, Training and Development, Philip R. Lee Institute for Health Policy Studies, University of California, San Francisco


Elizabeth BoydElizabeth Boyd, Ph.D., Associate Vice Chancellor, Ethics and Compliance; Program Director, Regulatory Knowledge and Support Program, CTSI; Associate Adjunct Professor, Social and Behavioral Science, University of California, San Francisco


Sara DrySarah Dry, M.D., Co-Director, Translational Pathology Core Laboratory; Associate Professor, Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles

EngageUC is an NIH-funded project to advance biorespository research among 5 University of California medical centers that collectively serve approximately 12 million individuals across the state. The 3-year project will develop uniform biorepository operations and harmonized biorepository governance practices for sample and data handling, system-wide IRB and regulatory approvals, best practices to consent outpatients for remnant sample collection, and ongoing relationships with California’s diverse communities via an innovative community engagement component.

2:25 The Era of Clinical Whole Genome Sequencing and Personalized Medicine

Joseph P. JarvisJoseph P. Jarvis, Ph.D., Senior Research Scientist, Coriell Institute for Medical Research

Access to patient genomic information will become increasingly important as physicians are progressively more receptive to incorporating genomics into routine clinical practice. When a patient needs a new prescription, it will be necessary for the physician to quickly and securely access your genetic data to understand drug efficacy prior to dosing. Who will patients and medical professionals trust to store and interpret the data? Coriell and the CPMC research study have defined several of the key barriers to accelerate the adoption and routine use of genomics in medicine and proposed effective solutions that are generally applicable.

3:00 Afternoon Refreshment Break

Genome Interpretation Software Solutions 

3:20 Software Spotlights (Sponsorship Opportunity Available)

Obtaining clinical genome data is rapidly becoming a reality but analyzing and interpreting the data continues to be a bottleneck. While there are many commercial software solutions and pipelines for managing raw genome sequence data, providing the medical interpretation and delivering a clinical diagnosis will be the critical step in making good on the promise of genomic medicine. This session will showcase how genome data analysis companies are streamlining the genomic diagnostic pipeline through:

•Transferring raw sequencing data
•Interpreting genetic variations
•Building new software and cloud-based analysis pipelines
•Investigating the genetic basis of disease or drug response
•Integrating with other clinical data systems
•Creating new medical-grade databases
•Reporting relevant clinical information in a physician-friendly manner
•Continuous learning feedback

Personalis3:20 Finishing the Clinical Exome and Accurate Interpretation: Key Challenges and Solutions

Richard Chen, M.D., CSO, Personalis Inc.

Diagnostic uncertainty can result from accuracy issues in next generation sequencing and interpretation.  In this talk, we will discuss technologies that Personalis has developed for solving key accuracy challenges in NGS including our gold standard genome, ACE technology for finishing the clinical exome, an advanced pipeline for calling structural variants, and an improved reference genome.  These technologies, together with proprietary, curated disease variant and pharmacogenomic databases, allow Personalis to provide highly accurate next generation sequencing and interpretation services. 

Real Time Genomics
3:35 You Can't Interpret What You Don't See:  Accurate and Fast Variant and de novo Mutation Identification from NGS Data

Francisco M. De La Vega, D.Sc., Vice President, Genome Science, Real Time Genomics

Identifying variants from NGS data persistently results in false negatives and positives, confounding downstream analysis and interpretation. We developed a solution that leverages family relationships to fast and accurately identify variants and de novo mutations in trios, reducing false negatives. Exome data can be aligned and called in just hours.

Strand_US3:50 Shortening the Diagnostic Odyssey

Ramesh HariharanRamesh Hariharan, Ph.D., Founder & Chief Technologist, Strand Life Sciences

This talk will describe our experiences at Strand in using genomic sequencing and bioinformatics techniques to shorten the odyssey to diagnosis for rare disease cases. Inspired by these cases, we are building  integrated software that combines curated literature content, bioinformatics databases, and various algorithms and user interfaces to substantially compress time taken and make it easier for clinicians to determine likely candidate variants in a Diagnostic Odyssey. The talk will provide glimpses of this software as well. 

4:05 CollabRxInterpretive Analytics of Big Data in Oncology by Physicians, for Physicians: Supporting Clinical Decision-Making at the Point of Care

Gavin Gordon Gavin J. Gordon, Ph.D., Head, Business Development & Alliances, CollabRx, Inc.

Cancer treatment and research is experiencing an unprecedented explosion of new knowledge, driven by the falling costs of DNA sequencing, that is outpacing clinical interpretation. This presentation will describe solutions developed by CollabRX that enable clinicians and patients to stay current and use this knowledge to inform cancer treatment planning.


4:20 SVBioTurnkey Next-Generation Diagnostics

Dietrich StephanDietrich A. Stephan, Ph.D., CEO, SV Bio

SV Bio has created a platform which allows users of DNA-based diagnostic information to access the advantages of next-generation technologies to improve the speed, accuracy, cost and sensitivity improvements. We have developed a turn-key platform, and will describe the nuances of the technology as well as how customers can access the service.


4:35 SimulConsultAutomated Genome-Phenome Analysis to Solve the Clinical Interpretation Bottleneck

Michael SegalMichael Segal, M.D., Ph.D., Founder & Chief Scientist, SimulConsult

State-of-the-art clinical diagnostic decision support is combined with analysis of an annotated genome variant table to result in an integrated genome-phenome analysis that assesses known human phenotypes. The output includes gene pertinence scores that remain robust when the phenotype is unusual or results from the action of two different genes. Processing times of seconds are followed by manual review times of ~30 minutes, thereby removing the clinical interpretation bottleneck for genome analysis.

5:05 Close of Session

5:20 Welcome Reception in the Exhibit Hall with Poster Viewing

6:30 Close of Day

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