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

June 25-28, 2013

Bio-IT World & Cambridge Healthtech Institute’s Second Annual
TCGC:  The Business of Integration and Implementation


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Thursday, June 27

7:30 am Conference Registration and Morning Coffee

Policy, Privacy and Patient Care 

8:30 Chairperson’s Opening Remarks

John Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina

8:40 Keynote Presentation 

Regulatory Considerations and Challenges for Ultra-High-Throughput Sequencing-Based Clinical Applications

Živana TežakŽivana Težak, Ph.D., Associate Director, Science and Technology, Personalized Medicine, Office of In Vitro Diagnostic Device Evaluation and Safety (OIVD), Center for Devices and Radiological Health (CDRH), FDA

The use of diagnostic tests that determine genetic sequence variation to guide patient care is rapidly expanding. At the same time, this rapid development of genomic sequencing technology and applications is raising new policy and regulatory questions. Some of the questions include efficient approaches for adequate demonstration of analytical performance. While there are no broadly accepted standards or methods to analytically validate ultra-high-throughput sequencing tests yet, there are a number of efforts underway, including establishing reference material that can aid in assessing analytical performance. The additional challenge in informed clinical application of sequencing information is inadequate knowledge about correlations between genomic variations and their clinical significance. Although there is a wealth of data being generated about genetic variation, a lot of it is fragmented and there is a need for concerted efforts to curate and organize this knowledge in a way that can support its clinical use. FDA is taking a number of steps to encourage cross-collaboration in this area, to be able to balance public safety concerns with fostering innovation and enabling the translation of emerging technologies that can improve medical care and benefit public health.

9:25 The Current State of Gene Patents

John ConleyJohn Conley, J.D., Ph.D., William Rand Kenan, Jr. Professor of Law, University of North Carolina

This presentation will analyze the current state and likely future of gene patents. A primary focus will be on the ongoing AMP vs. Myriad Genetics case, now before the Supreme Court, which is the first case to raise squarely the question of whether and in what forms DNA sequences can be patented. A decision is possible before the conference, so the presentation may be able to provide a timely report on what the Court has decided. The presentation will also review other, less publicized ways in which gene patents have been effectively challenged, including through the nonobviousness and written description requirements. Moreover, current and future sequencing technologies may be bypassing single-gene patent claims, rendering them less valuable regardless of what the Supreme Court decides, and motivating companies to seek other kinds of commercial advantages. Myriad Genetics’ announced business strategy for Europe will be discussed as a reflection of this new reality.

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

10:45 Privacy and Progress in Whole Genome Sequencing: The Presidential Commission Report

Elizabeth PikeElizabeth Pike, J.D., LL.M., Senior Policy and Research Analyst, Presidential Commission for the Study of Bioethical Issues

In October 2012, the Presidential Commission for the Study of Bioethical Issues released its report Privacy and Progress in Whole Genome Sequencing. The report concludes that to realize the enormous promise that whole genome sequencing holds for advancing clinical care and the greater public good, individual interests in privacy must be respected and secured. The Commission offers 12 recommendations to help craft policies that are flexible enough to ensure progress and responsive enough to protect privacy. In this session, we will discuss some of the ethical and privacy concerns raised by the increased use of whole genome sequencing and the ways that the Commission chose to address these concerns.

11:20 Mapping the Next-Generation Sequencing Industry

Maggie CurnutteMargaret Curnutte, Ph.D., Research Fellow, Baylor College of Medicine

This presentation provides an overview of the emerging business models within the next-generation sequencing industry. From sequencing to variant calling to annotating and analyzing and data storage, companies in this area of innovation are developing and/or pairing such features in novel ways that challenge policy implications for the clinic. These implications will be discussed with reference to the current regulatory landscape for genetic testing technologies.

11:55 Close of Session

genia12:00 pm Luncheon Presentation: What Happens When Sequencing Becomes Really Cheap, Really Easy, and Really Fast? 

Stefan RoeverStefan Roever, CEO & Founder, Genia Technologies

There is no debate that genetic information is needed to truly realize the promise of personalized medicine.  The problem is that today’s DNA sequencers cost anywhere from $50K - $1M and utilize a complex workflow that does not lend itself to clinical utility.  Genia is using standard semiconductor technology to enable massively parallel, single molecule DNA sequencing.  The company has developed a versatile nanopore-based platform which allows for single molecule, electrical, real-time analysis. 

1:15 Chairperson’s Remarks

Shawn C. Baker, Ph.D., CSO, BlueSEQ

The Clinical Genome Technology Showcase

The success of producing As, Cs, Gs, and Ts at exponentially lower costs, along with longer and more accurate reads, is revolutionizing genomic diagnostic medicine. Thus, the promise of next-generation sequencing has shifted from discovery to clinical utility. Now the question is: how do we best use this sequence information in patient care? Hear first-hand from the companies that continue to drive the genomics revolution.

N-of-One1:20 - 1:35 Interpreting Molecular Data from Sequencing Platforms with Leading Edge Knowledge for Treatment and Diagnostic Options

Jennifer Carter, Founder & CMO, N-of-One, Inc.

Physicians, labs, institutions and patients can efficiently make the best diagnostic and treatment choices,   The PrecisionWorks framework enables experts to translate molecular data specific to each patient and the extensive available knowledge for each cancer type into state-of-the-art, clinically actionable insights and therapeutic options focused at the point of care.

Illumnia logo1:35 - 2:05 Clinical Interpretation of Genomes in Healthy Individuals

Carri-Lyn Mead, Ph.D., Scientist 2, Illumina, Inc.


Complete Genomics2:05 - 2:35 Finally!  Easy Access to Whole Human Genomes

Julie AdamsJulie Adams, Vice President, Product Management, Complete Genomics

Complete is developing software to deliver genomic information from any and all sources in an actionable, personalized form. As a first step,Genome Voyager™ is now available as an educational tool that enables researchers and academics to gain first-hand experience analyzing whole human genomes. After joining the Genome Voyager community, users can visualize and explore published whole human genomes. Users also have the opportunity to collaborate with colleagues and discuss their findings.

Wafergen2:35 - 3:05 The Pursuit of Higher Accuracy and Precision in Clinical Next Generation Sequencing  –  the SmartChip TE™ Target Enrichment System

Jude_DunneJude Dunne, Ph.D., Vice President, Product Development, WaferGen

The clinical sequencing community has been grappling with the transfer of ngs sequencing tests from development into the clinic. Recommendations from working groups have highlighted accuracy and precision as key attributes for successful introduction of tests into the clinical CLIA environment. To meet this challenge WaferGen has developed the high-density SmartChip TE System. Practical benefits of this methodology include flexibility in panel development, improved accuracy and precision with a simple, intuitive, lab-friendly workflow.

Life_Technologies3:05 - 3:35 Integrated NGS Sequencing and Reporting Using the Ion Torrent Platform

Mike Lelivelt, Ph.D., Director, Bioinformatics & Software Products, Ion Torrent, part of Life Technologies

As next generation sequencing prepares for a move from the research bench to future clinical applications, Ion Torrent is building systems to support the routine acquisition of sequencing data.  Torrent Suite Software is designed for easy, routine control of the Ion Torrent Personal Genome Machine as well as monitoring data quality control covering the fundamentals of sequencing performance.  Following acquisition read data in Torrent Suite Software, data can be transferred to Ion Reporter Software in a streamlined automated manner.  Ion Reporter Software offers both mapping and variant calling using a controlled, role-based workflow with integrated audit trails.  Variants called within Ion Reporter are labeled with rich annotation sources from public repositories.  Easy to use filters enable data to be reduced done to the variants of greatest impact.  Decision support functionality within Ion Reporter Software allows technicians to classify variants into a formal report structure.  External annotation sources, such as Ingenuity and Compendia Cancer Annotations, are integrated into Ion Reporter to allow increased variant knowledge to be directly available for incorporation into variant reports. 


3:35 Refreshment Break in the Exhibit Hall with Poster Viewing

Genomic Data Integration 

4:15 The New NIH Genetic Testing Registry: Bringing Together Science, Medicine and Policy

Wendy RubinsteinWendy Rubinstein, M.D., Ph.D., Senior Scientist and Director, NIH Genetic Testing Registry, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health

Dr. Rubinstein will introduce the GTR, a free online resource that provides centralized access to comprehensive genetic test information that is voluntarily submitted by test providers. She will survey the content of GTR including registered laboratories, accessioned tests for heritable conditions, and the quality measures and evidentiary basis of the tests. NCBI’s representation of information about clinically relevant variants will also be discussed.

4:45 Selected Oral Poster Presentation: Control-Free Tumour Analysis with Galaxy

Andrew Stubbs, Ph.D., Assistant Professor, Bioinformatics, Erasmus University Medical Center

The first step in tumour analysis is typically a correction with a normal sample, taken from healthy tissue of the same individual. The majority of variants (80%-95%) found in a tumour sample are germline mutations also found in the healthy tissue. When such an associated normal sample is not available, a different filtering method must be employed. Because the majority of variants found in an individual are common throughout the population, we have constructed a set of 85 samples from healthy, unrelated individuals, to act as a “virtual normal.” We tested our “virtual normal” somatic variant detection approach on two public breast cancer datasets, and two in-house prostate cancer samples, both sequenced on the Complete Genomics platform. We compared the results of this analysis to a standard tumour/normal analysis to detect somatic variations for both structural variations (SVs) as well as SNVs and small indels and substitutions. In addition, the results for both analyses were filtered for variants present in several databases of human variation, including the 1000 Genomes project, dbSNP and the Exome Variant Server. We have implemented the tools used for this data analysis in a user-friendly Galaxy, which is deployed in CLOUD environment, to allow for instant scale-up and provide resources for large experimental studies from translational research scientists. Our results suggest that this “virtual normal” approach can act as a substitute for an associated normal sample, eliminating the need to sequence a matching normal sample for every tumour sample. We will provide a summary of our cancer genome analysis and the associated analytical workflows we developed to support cancer research using our Galaxy/CLOUD and our fusion gene viewer, iFUSE, for the detection of candidate fusion genes.

5:15 Evening Reception

6:30 Close of Day

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