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The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
The Clinical Genome Conference 2014
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The Clinical Genome Conference 2014

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This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of …

This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com

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  • 1. Advance Savings up to $200! Register by May 2 for Hotel Kabuki, San Francisco, CA June 10 - 12, 2014 FINAL AGENDA CLINICALGENOMEconference THE 3rd ANNUAL Mining the Genome for Medicine ClinicalGenomeConference.com TCGC The unstoppable march of genomics into clinical practice continues. In an ideal world, the expanding use of genomic tools will identify disease before the onset of clinical symptoms and determine individualized drug treatment leading to precision medicine. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances and actionable patient care. Join vital discussions of the applications, questions and solutions surrounding clinical genome analysis. KEYNOTE SPEAKERS Atul Butte, M.D., Ph.D. Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital David Galas, Ph.D. Principal Scientist, Pacific Northwest Diabetes Research Institute Gail P. Jarvik, M.D., Ph.D. Head, Division of Medical Genetics, Arno G. Motulsky Endowed Chair in Medicine and Professor, Medicine and Genome Sciences, University of Washington Medical Center John Pfeifer, M.D., Ph.D. Vice Chair, Clinical Affairs, Pathology and Immunology; Professor, Pathology and Immunology, Washington University John Quackenbush, Ph.D. Professor, Dana-Farber Cancer Institute and Harvard School of Public Health; Co-Founder and CEO, GenoSpace Topics Include: • Working with the Payer Process • Genome Variation and Clinical Utility • NGS Is GuidingTherapies • NGS Is Redefining Genomics • Interpretation andTranslation to the Client • Integrating Genomic Data into the Clinic Corporate Sponsors: Co-Sponsored by: Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com
  • 2. Pre-Conference Dinner Short Courses* MONDAY, JUNE 9 1:30 pm Short Course Registration 2:00-5:30 (SCa) Hadoop and High-Dimensional Data Mining in the Era of the Clinical Genome The exponential decline in the cost of next generation sequencing is making it possible to discover rare genetic variants that may explain rare childhood diseases and cancer.To detect these rare variants requires the aggregation and analysis of genomics and clinical data at scale. Meanwhile, the advent of Hadoop, a programming framework that supports the processing of large data sets in a distributed computing environment, is driving the re-thinking and re-design of traditional data mining approaches. During this short course, we will briefly review key Hadoop concepts, and highlight how Hadoop makes novel data mining applications possible. Session speakers will share novel data mining strategies and approaches such as topological data analysis (TDA) and massively parallel database processing to perform a spectrum of genomic and clinical analyses. What’s Hadoop and Does It Matter for My Genome Interpretation? E Sasha Paegle, Senior Business Development Manager, Life Sciences, Isilon Storage Division, EMC² It’s no surprise to hear the word “Hadoop” when discussing the latest data mining strategies. But what is Hadoop? What are the advantages and disadvantages of Hadoop? During this short course we will introduce key Hadoop concepts, highlight where Hadoop is used in biomedical informatics and discuss how Hadoop makes it possible to introduce a new era of data mining applications for clinical genomics. Genomics with Query: Re-ThinkingAnalytics for the Clinical Setting Sarah Aerni, Ph.D., Senior Data Scientist, Pivotal Effective analysis and understanding of patient genomes requires integration and processing of large and diverse patient datasets. We will cover our work in speeding up genomics pipelines by leveraging Pivotal’s Hadoop and MPP database technologies and conclude with our approaches in the analysis, integration and visualization of genomics and clinical data. Unfolding the Shape of Clinical Genomics Eithon Cadag, Ph.D., Principal Data Scientist, Ayasdi Comprehensive exploration of modern genomic data is challenging; new technologies provide myriad and massive datasets. As these data find application in clinical domains, difficulty and urgency is multiplied. In this session, we will discuss broad application of topological data analysis (TDA), a growing subfield of mathematics, to address fundamental data problems in clinical genomics. 4:30 Short Course Registration 5:00-5:30 Shared Dinner Buffet 5:00-8:30 (SC1) Implementing Next-Generation Sequencing for Clinical Diagnostics The rapid evolution of next-generation sequencing and the resulting move into routine clinical practice requires arguably as much skill in navigating through new unchartered territories of clinical testing as the sequence generation, bioinformatics and interpretation of variants. Significant challenges for clinical diagnostics include the rapid evolution of platforms, protocols, kits and reagents as well as genome analysis, interpretation and ethics.This short course provides practical information on implementing clinical sequencing, genomic data analysis and interpretation, ethics and proficiency testing. Next Generation of Operational Challenges for Implementing Clinical Genomics in Genetics Laboratories Mike M. Moradian, Ph.D., Director of Operations and Molecular Genetics Scientist, Kaiser Permanente Southern California Regional Genetics Laboratory Clinical genomics has become a reality in today’s complex and dynamic molecular pathology laboratory setup, which requires detailed operational planning and oversight. Laboratories could face many challenges when deciding to implement clinical genomics, including preanalytical (e.g., appropriate test orders, testing platforms, staff training), analytical (e.g., assay validation, quality control, result generation) and post-analytical (e.g., bioinformatics expertise, result interpretation, preparation of an appropriate report for physician/clinic use). Of course, regulatory, compliance and billing/reimbursement issues are vital to the survival of such operations. A brief description of these operational challenges and possible solutions will be discussed. Adventures in the Land of Clinical Sequencing: Implementation of Next-Generation Sequencing-BasedTests in a CAP-Regulated Laboratory Avni B. Santani, Ph.D., Assistant Professor, Clinical Pathology, Perelman School of Medicine, University of Pennsylvania and Scientific Director, Molecular Genetics Lab The learning objectives of this presentation include: 1) Outline the strategy geared towards practical implementation of a genomics program in a molecular diagnostic laboratory, 2) Review the development and validation of next-generation sequencing-based tests, including panels and whole-exome sequencing and 3) Examine the impact of implementing NGS-based tests on the clinical laboratory. Automation of Sample Preparation for Clinical NGS:The Requirements and the Challenges for CLIA-Certified Clinical Laboratories Martin Siaw, Ph.D., MB(ASCP) CM , Associate Scientific Director, Advanced Sequencing, Quest Diagnostics Nichols Institute Sample preparation is an important component of any molecular testing that is being done in clinical laboratories. With the increasing use of NGS for clinical testing comes the need to process increasingly larger numbers of patient samples. Automation of sample preparation should be considered to be critical to the workflow of diagnostic tests involving the use of NGS. My presentation will focus on the requirements and challenges for CLIA-certified clinical laboratories. Additional Instructors to be Announced Dinner Short Courses* WEDNESDAY, JUNE 11 6:00 pm-9:00 pm (SC2)VariantAnalysis and Contribution to Disease Advances in NGS have provided unprecedented opportunities to mine genetic data from individuals to populations.The subsequent identification of genetic variants which may be implicated in disease is an important step in linking sequence data with disease and provides new approaches to improve human health. In this course you will explore genetic data science, an emergent discipline that seeks to deliver better answers from the data so that patients and their physicians can determine informed healthcare decisions. Using Chromatin Contacts to Create High-Contiguity GenomeAssemblies Joshua N. Burton, Research Scientist, Jay Shendure Laboratory, Genome Sciences, University of Washington To study genetics and population variation in any new species, we must first sequence its genome. But de novo genome assemblies created from short next-generation reads are highly fragmented. We have developed a method to create chromosome-scale scaffolds in de novo genome assemblies by exploiting chromatin interaction datasets. Our method is cost-effective, scalable and generalizable to any species. Detecting Indels and StructuralVariants in the Clinical Setting KaiYe, Ph.D., Research Assistant Professor, Genetics,The Genome Institute, Washington University High-performance analysis tools for short indels and complex structural variants are demanded for clinical applications. Currently medium-sized indels and structural variants are often missed by standard pipelines like GATK but often contribute to disease. Here, the best practices for detecting those missing variants are described. ExtensiveVariation in Chromatin StatesAcross Humans Maya Kasowski, Ph.D., Research Scientist, Mike Snyder Laboratory, Genetics, Stanford University The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence and is associated with disruptions of transcription factor binding motifs. * Separate Registration Required shortcourses Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 3. TUESDAY, JUNE 10 7:30 am Conference Registration and Morning Coffee Working with the Payer Process 8:30 Chairperson’s Opening Remarks »»KEYNOTE PRESENTATION 8:45 Case Study onWorking through the Payer Process John Pfeifer, M.D., Ph.D., Vice Chair, Clinical Affairs, Pathology; Professor, Pathology and Immunology; Professor, Obstetrics and Gynecology, Washington University School of Medicine If next-generation sequencing (NGS) is to become a part of patient care in routine clinical practice (whether in the setting of oncology or in the setting of inherited genetic disorders), labs that perform clinical NGS must be reimbursed for the testing they provide. Genomics and Pathology Services at Washington University in St. Louis (GPS@WUSTL) will be used as a case study of a national reference lab that has been successful in achieving high levels of reimbursement for the clinical NGS testing it performs, including from private payers.The reasons for GPS’s success will be discussed, including NGS test design, clinical focus of testing, use of different models for reimbursement and payer education. 9:30 Implementation of Clinical Cancer Genomics within an Integrated Healthcare System Lincoln D. Nadauld, M.D., Ph.D., Director, Cancer Genomics, Intermountain Healthcare Precision cancer medicine involves the detection of tumor-specific DNA alterations followed by treatment with therapeutics that specifically target the actionable mutations. Significant advances in genomic technologies have now rendered extended genomic analyses of human malignancies technologically and financially feasible for clinical adoption. Intermountain Healthcare, an integrated healthcare delivery system, is taking advantage of these advances to programmatically implement genomics into the regular treatment of cancer patients to improve clinical outcomes and reduce treatment costs. 10:00 PANEL DISCUSSION: Payer’s Dilemma: Evolution vs. Revolution As falling genome sequencing costs help clinicians refine patient diagnoses and therapeutic approaches, new complexities arise over insurance coverage of such tests, classification by CPT codes and other reimbursement issues. Experts on this panel will discuss payer challenges and changes—both rapid and gradual—occurring alongside these advances in clinical genomics. Moderator: KatherineTynan, Ph.D., Business Development & Strategic Consulting for Diagnostics Companies,Tynan Consulting LLC Panelists: Tonya Dowd, MPH, Director, Reimbursement Policy and Market Access, Quorum Consulting Mike M. Moradian, Ph.D., Director of Operations and Molecular Genetics Scientist, Kaiser Permanente Southern California Regional Genetics Laboratory Rina Wolf, Vice President of Commercialization Strategies, Consulting and Industry Affairs, XIFIN Additional Panelists to be Announced 10:45 Networking Coffee Break 11:15 Beyond Genomics: Preparing for theAvalanche of Post-Genomic Clinical Findings Jimmy Lin, M.D., Ph.D., President, Rare Genomics Institute Whole genomic and exomics sequencing applied clinically is revealing newly discovered genes and syndromes at an astonishing rate. While clinical databases and variant annotation continue to grow, much of the effort needed is functional analysis and clinical correlation. At RGI, we are building a comprehensive functional genomics platform that includes electronic health records, biobanking, data management, scientific idea crowdsourcing and contract research sourcing. 11:45The MMRF CoMMpass ClinicalTrial:A Longitudinal Observational Trial to Identify Genomic Predictors of Outcome in Multiple Myeloma Jonathan J. Keats, Ph.D., Assistant Professor, Integrated Cancer Genomics Division,Translational Genomics Research Institute 12:15 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch onYour Own Genome Variation and Clinical Utility 1:45 Chairperson’s Remarks »»KEYNOTE PRESENTATION 1:50 Lessons from the Clinical Sequencing Exploratory Research (CSER) Consortium: Genomic Medicine Implementation Gail P. Jarvik, M.D., Ph.D., Head, Division of Medical Genetics, Arno G. Motulsky Endowed Chair in Medicine and Professor, Medicine and Genome Sciences, University of Washington Medical Center Recent technologies have led to affordable genomic testing. However, implementation of genomic medicine faces many hurdles.The Clinical Sequencing Exploratory Research (CSER) Consortium, which includes nine genomic medicine projects, was formed to explore these challenges and opportunities. Dr. Jarvik is the PI of a CSER genomic medicine project and of the CSER coordinating center. She will focus on the frequency of exomic incidental findings, including those of the 56 genes recommended for incidental finding return by the ACMG.The CSER group has annotated the putatively pathogenic and novel variants of the Exome Variant Server (EVS) to estimate the rate of these in individuals of European and African ancestry. Experience with consenting and returning incidental findings will also be reviewed. 2:35 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. 3:05AnalyzingVariants with a DTC Genetics Database Brian Naughton, Ph.D., Founding Scientist, 23andMe, Inc. Sequencing a genome results in dozens of potentially disease-causing variants (VUS). I describe some examples of using the 23andMe database, including quick recontact of participants, to determine if a variant is disease-causing. 3:35 Refreshment Break in the Exhibit Hall with PosterViewing Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 4. Genome Interpretation Software Solutions: Software Spotlights (Sponsorship Opportunities Available) Obtaining clinical genome data is rapidly becoming a reality, but analyzing and interpreting the data remains 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 fulfilling 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 4:15 Software Spotlight #1 4:30 Copy NumberVariant Detection Using Sponsored by Next-Generation Sequencing: State of the Art Alexander Kaplun, Ph.D., Field Applications Scientist, BIOBASE This talk will provide a short review about the current state of the art in detection of larger variants that have an important role in many diseases such as haplotypes, indels, repeats, copy number variants (CNVs), structural variants (SVs) and fusion genes using NGS methods, and an outlook to their use for pharmacogenomic genotyping. 4:45 Software Spotlight #3 5:00 Software Spotlight #4 5:15 Software Spotlight #5 5:30 Pertinence Metric Enables Hypothesis-Independent Sponsored by Genome-Phenome Analysis in Seconds Michael M. Segal, M.D., Ph.D., Chief Scientist, SimulConsult Genome-phenome analysis combines processing of a genomic variant table and comparison of the patient’s findings to those of known diseases (“phenome”). In a study of 20 trios, accuracy was 100% when using trios with family-aware calling, and close to that if only probands were used.The gene pertinence metric calculated in the analysis was 99.9% for the causal genes.The analysis took seconds and was hypothesis-independent as to form of inheritance or number of causal genes. Similar benefits were found in gene discovery situations. 6:00Welcome Reception in the Exhibit Hall with PosterViewing 7:00 Close of Day WEDNESDAY, JUNE 11 7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee NGS Is GuidingTherapies 8:30 Chairperson’s Opening Remarks 8:35 Next-Generation SequencingApproaches for Identifying Patients Who May Benefit from PARP InhibitorTherapy Mitch Raponi, Ph.D., Senior Director and Head, Molecular Diagnostics, Clovis Oncology The following questions will be addressed: What biomarkers should we be focusing on to identify appropriate patients who will likely benefit from PARP inhibitors? How can we apply next-generation sequencing technologies to identify all patients who will respond to the PARP inhibitor rucaparib? What regulatory challenges are we faced with for approval of NGS companion diagnostics? 9:05Whole-Genome andWhole-Transcriptome Sequencing to Guide Therapy for Patients withAdvanced Cancer Glen J. Weiss, M.D., MBA, Director, Clinical Research, CancerTreatment Centers of America Treating advanced cancer with agents that target a single-cell surface receptor, up-regulated or amplified gene product or mutated gene has met with some success; however, eventually the cancer progresses. We used next-generation sequencing technologies (NGS) including whole-genome sequencing (WGS), and where feasible, whole-transcriptome sequencing (WTS) to identify genomic events and associated expression changes in advanced cancer patients. While the initial effort was a slower process than anticipated due to a variety of issues, we demonstrated the feasibility of using NGS in advanced cancer patients so that treatments for patients with progressing tumors may be improved.This lecture will highlight some of these challenges and where we are today in bringing NGS to patients. 9:35The SmartChipTE™Target Enrichment System for Sponsored by Clinical Next-Gen Sequencing Gianluca Roma, MS MBA, Director, Product Management, WaferGen Biosystems 10:05 Coffee Break in the Exhibit Hall with PosterViewing Data Mining »»KEYNOTE PRESENTATION 10:45Translating aTrillion Points of Data into Therapies, Diagnostics and New Insights into Disease Atul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital; Co-Founder, Personalis and Numedii There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations have been well described.The nascent field of translational bioinformatics may help. Dr. Butte’s lab at Stanford builds and applies tools that convert more than a trillion points of molecular, clinical and epidemiological data— measured by researchers and clinicians over the past decade—into diagnostics, therapeutics and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab’s work on using publicly available molecular measurements to find new uses for drugs, including drug repositioning for inflammatory bowel disease, discovering new treatable inflammatory mechanisms of disease in type 2 diabetes and the evaluation of patients presenting with whole genomes sequenced. 11:30 DGIdb – Mining the Druggable Genome Malachi Griffith, Ph.D., Research Faculty, Genetics,The Genome Institute, Washington University School of Medicine In the era of high-throughput genomics, investigators are frequently presented with lists of mutated or otherwise altered genes implicated in human disease. Numerous resources exist to generate hypotheses about how such genomic events might be targeted therapeutically or prioritized for drug development.The Drug-Gene Interaction database (DGIdb) mines these resources and provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially druggable genes. DGIdb can be accessed at dgidb.org. 12:00 pm Sponsored Presentation (Opportunity Available) 12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch onYour Own Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 5. NGS Is Redefining Genomics 2:00 Chairperson’s Remarks »»KEYNOTE PRESENTATION 2:05 Extra-Cellular RNA: AWindow into New Biological Phenomena David Galas, Ph.D., Principal Scientist, Pacific Northwest Diabetes Research Institute In recent years it has become clear that various body fluids, outside cells, contain a wide range of RNA molecules (exRNA). Included are microRNAs, but many others types are represented as well. Stable circulation of RNA is facilitated by binding to certain proteins and/or protection within microvesicles and exosomes. While the function of cell-to-cell communication for these molecules is implicated by new evidence, the roles of most of them remain ambiguous. Recent evidence that microbial RNA is included in the exRNA spectrum in plasma raises a number of intriguing questions and heightens awareness of the need to understand the origins, fates and functions of the wide range of circulating RNA. 2:50 Harnessing Single-Cell -Omics to Reveal Diversity and Mosaicism in the Brain Jennifer Erwin, Ph.D., Research Scientist, Fred H. Gage Laboratory, Genetics,The Salk Institute for Biological Studies It is now known that retrotransposition of LINE-1 mobile elements contributes genomic diversity to mouse and human neurons.The unique composition of genetic mosaicism present in the brain may contribute to disease and also the behavior differences observed between genetically identical organisms. Because each individual neuron has the potential to have a unique genome, single-cell approaches are essential to measure and observe this genomic diversity, which is obscured in bulk samples. We will present data using single-cell genome and transcriptome sequencing to characterize the nature and regulation of neuronal genome mosaicism. 3:20 Sponsored Presentation (Opportunity Available) 3:50 Refreshment Break in the Exhibit Hall with PosterViewing 4:25Analysis of Germline GenomeVariation and MosaicVariants in SomaticTissues Using Integrated NGS- and PCR-BasedTechnology Alexander Eckehart Urban, Ph.D., Assistant Professor, Department of Psychiatry and Behavioral Sciences and Department of Genetics (secondary), Center for Genomics and Personalized Medicine, Stanford University School of Medicine We are investigating genome variants that affect brain development and function. We study germline variants that are associated with mental disorders and also the occurrence of genomic mosaicism in somatic tissue. We are using both tissue culture models and primary tissue samples in combination with next-generation sequencing-based approaches, targeted- capture and whole-genome, respectively, as well as PCR-based methods such as standard PCR, qPCR and digital droplet PCR. »»KEYNOTE PRESENTATION 4:55 From Big Data to Network Medicine John Quackenbush, Ph.D., Professor, Dana-Farber Cancer Institute and Harvard School of Public Health; Co-Founder and CEO, GenoSpace The sequencing of the human genome promised to open new ways of understanding human disease. New sequencing technologies, which have driven the cost of whole-genome sequencing to a few thousand dollars, have begun to make this vision a reality, allowing not only an integrated view of disease but also new ways of modeling the processes that drive it. We will describe methods that have begun to allow the creation of disease-specific network models and to extend these to modeling processes in individual patients. 5:40 Close of Day 5:30-6:00 Dinner Short Course Registration 6:00-9:00 Dinner Short Course (see page 2 for details) THURSDAY, JUNE 12 7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee NGS References and Standards Are Not Static 8:30 Chairperson’s Opening Remarks 8:35 Making Sense of Updates to the Human Reference Genome Assembly Valerie A. Schneider, Ph.D., Staff Scientist, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health The human reference genome assembly, whose sequence was first published more than a decade ago, is not static.The Genome Reference Consortium (GRC) manages updates to the reference assembly that reflect our improving understanding of genomic biology and recently released a major assembly update, GRCh38. We will review updates to the reference assembly and discuss their implications for sequence analysis, variant identification and clinical interpretation. NCBI-developed tools that assist users with interrogation and visualization of the assembly will also be discussed. 9:05 Genome in a Bottle: Reference Materials to EnableTranslation Marc Salit, Ph.D., Group Leader, Biochemical Science and Multiplexed Biomolecular Science, National Institute of Standards andTechnology (NIST) The Genome in a Bottle Consortium has been developing reference materials, data and methods to support translation of sequencing to regulated clinical practice.These materials and data played a key role in the first FDA authorization of a “next-generation” DNA sequencer, bringing this technology into a new era of clinical care. We will present a perspective on the consortium projects and products, and a projection for future genomic references. 9:35 StandardizingVariant Files for Clinical Diagnostics Karen Eilbeck, Ph.D., Associate Professor, Biomedical Informatics, University of Utah While variant files are the currency for personal genome information, there exists much polymorphism in how the variant file formats are implemented, making sharing and comparison difficult between labs.The CDC convened a work group to provide recommendations for standard variant file practices for clinical diagnostics.This work and the group’s recommendations will be presented. 10:05 Coffee Break in the Exhibit Hall with PosterViewing Interpretation andTranslation to the Client 10:45 Making Meaning of Genomic Data: Clinical Interpretation and Communication Julianne M. O’Daniel, MS, CGC, Assistant Professor, Genetics, University of North Carolina at Chapel Hill Genome sequencing has been rapidly adopted for use in complex genetic diagnoses. The ability to cast such a broad net for analysis, however, raises questions about clinical interpretation and identifying “best fit” variant(s) based on current knowledge and phenotype data. Decisions must be made about what to report and why in terms of diagnostic and/or incidental findings. We will highlight salient issues in clinical interpretation from test definition and variant interpretation to patient expectations and understanding. Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 6. 11:15 Interpreting and Communicating the “Healthy” Genome Elissa Levin, MS, CGC, Head, Genomics and Integrative Health Innovations; Assistant Professor, Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine Most genome sequencing to date has focused on rare disease or diagnostic odyssey cases. But how will this technology impact the average person? And how are providers expected to keep up with and accurately communicate genomic data in the context of their patients? We will discuss some of the challenges with interpreting WGS in “healthy people” and some approaches to positively impacting the delivery of genomic information to both providers and patients. 11:45 PANEL DISCUSSION: Who Is the Client andWhat Should Be Returned? Genome sequencing technologies have enabled greater and faster genetic data collection for diagnostics—but what information should providers report to their clients and how should they translate it to patient needs?This panel of genetic counseling experts will discuss challenges of interpreting variants, incidental findings and other data, plus strategies for facilitating communication between and ensuring comprehension by providers and patients. Panelists: Julianne M. O’Daniel, MS, CGC, Assistant Professor, Genetics, University of North Carolina at Chapel Hill Elissa Levin, MS, CGC, Head, Genomics and Integrative Health Innovations; Assistant Professor, Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine Additional Panelists to be Announced 12:30 pm Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch onYour Own Integrating Genomic Data into the Clinic 1:30 Chairperson’s Remarks 1:35 Introducing Pharmacogenomics into Primary Care and Cardiology Settings: HowWill Clinicians Respond? Josh F. Peterson, M.D., MPH, Assistant Professor, Biomedical Informatics and Medicine, Vanderbilt School of Medicine, Vanderbilt University Digital representations of the human genome and its derivatives within electronic and personal health records are a foundation for 21st-century medicine, creating a new biological approach to more precise, targeted clinical decision making at the point of care. However, numerous translational challenges have hindered adoption, involving technical infrastructure, feasibility, demonstration of clinical effectiveness and sustainability.This talk will highlight how the development and implementation of a large pharmacogenomics program has addressed these challenges, highlighting the health information technology, laboratory and clinical processes which enable the program, and describe how clinicians have responded when presented with pharmacogenomics variants and the option of genome-tailored therapy for their patients. 2:05 Genomics into the Clinic: Ethical and Policy Challenges David Magnus, Ph.D., Director, Stanford Center for Biomedical Ethics;Thomas A. Raffin Professor, Medicine and Biomedical Ethics; Professor, Pediatrics, Stanford University School of Medicine The introduction of next-generation sequencing technology into clinical practice raises many ethical, policy and practical challenges.These include challenges to informed consent, new risks, privacy and issues of control over the disposition of information. In addition to normative analysis, data from early adopters can help shed light on ways of meeting these challenges. 2:35 Sponsored Presentation (Opportunity Available) 3:05 Refreshment Break, Last Chance for Exhibit and PosterViewing 3:45 Clinical Genomics in the Era of the EHR: Challenges and Opportunities Keith Marsolo, Ph.D., Associate Professor, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center and Associate Professor, Pediatrics, University of Cincinnati College of Medicine The electronic health record (EHR) provides potential benefits to the field of clinical genomics, including the ability to return results to the provider, use genetic findings for decision support purposes and serve as a source of phenotypic data. But not all EHR implementations are created equal. We will provide an overview of the different ways that data can be captured in the EHR, the role that EHR implementation plays on data quality and availability and the potential for integration of genetic findings in today’s EHR. We will conclude by discussing the minimum functional requirements that EHRs will need to satisfy in order to serve the field of clinical genomics. 4:15 PANEL DISCUSSION: Digitized Data for Clinical Utility and Primary Care To ensure that clinical genomic data is useful for the patients it is meant to serve, clinicians must overcome various technical, policy and ethical hurdles while leveraging health information technology.This panel of experts will discuss the electronic health record (EHR): how to integrate genomic data in it, the nature of that data, EHR infrastructure, functional requirements and more. Panelists: Fred Lorey, Ph.D., Representative, North American Council, International Society for Neonatal Screening; Member, U.S. Department of Health and Human Services Secretary’s Advisory Committee on Heritable Disorders in Newborns and Children (SACHDNC); former Acting Director, California Genetic Disease Screening Program, California Department of Public Health David Magnus, Ph.D., Director, Stanford Center for Biomedical Ethics;Thomas A. Raffin Professor, Medicine and Biomedical Ethics; Professor, Pediatrics, Stanford University School of Medicine Keith Marsolo, Ph.D., Associate Professor, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center and Associate Professor, Pediatrics, University of Cincinnati College of Medicine Josh F. Peterson, M.D., MPH, Assistant Professor, Biomedical Informatics and Medicine, Vanderbilt School of Medicine, Vanderbilt University Additional Panelists to be Announced 5:00 Close of Conference MEDIA PARTNERS Official Media Sponsor Lead Sponsoring Publications Sponsoring Publications Web Parnters Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 7. CHI offers comprehensive packages that can be customized to your budget and objectives. Sponsorship allows you to achieve your goals before, during, and long after the event. Packages may include presentations, exhibit space and branding, as well as the use of delegate lists. Signing on early will maximize your exposure to qualified decision- makers and drive traffic to your website in the coming months. Podium Presentations — Available within MainAgenda! Showcase your solutions to a guaranteed, targeted audience through a 15- or 30-minute presentation during a specific program, breakfast, lunch, or a pre-conference workshop. Package includes exhibit space, on-site branding, and access to cooperative marketing efforts by CHI. Lunches are delivered to attendees who are already seated in the main session room. Presentations will sell out quickly! Sign on early to secure your talk. Invitation-OnlyVIP Dinner/Hospitality Suite Select specific delegates from the pre-registration list to attend a private function at an upscale restaurant or a reception at the hotel. From extending the invitations, to venue suggestions, CHI will deliver your prospects and help you make the most of this invaluable opportunity. Focus Group CHI will gladly provide you the opportunity of running a focus group on-site.This exclusive gathering can be useful to conduct market research, collect feedback on a new product idea, and collect marketing intelligence from industry experts on a specific topic. User Group Meeting/Custom Event Co-locate your user group meeting or custom event. CHI will help market the event, manage logistical operations, develop the agenda, and more. CHI can handle the entirety of the meeting or select aspects. Exhibit Exhibitors will enjoy facilitated networking opportunities with qualified delegates, making it the perfect platform to launch a new product, collect feedback, and generate new leads. Exhibit space sells out quickly, so reserve yours today! Additional branding and promotional opportunities are available, including: • ConferenceTote Bags • Literature Distribution (Tote Bag Insert or Chair Drop) • Badge Lanyards • Program Guide Advertisement • Padfolios and More... sponsorship&exhibit opportunities For more information, please contact: Jay Mulhern Business Development Manager 781-972-1359 | jmulhern@healthtech.com tcgc Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 8. tcgc hotel&travel CONFERENCE VENUE & HOTEL: Hotel Kabuki 1625 Post Street San Francisco, CA 94115 Phone: 415.922.3200 | Reservation Line: 1-800-533-4567 Discounted Room Rate: $179 s/d Discounted Room Rate Cut-off Date: May 13, 2014 Please visit our conference website to make your reservations online or call the hotel directly to reserve your sleeping accommodations.You will need to identify yourself as a Cambridge Healthtech Institute conference attendee to receive the discounted room rate with the host hotel. Reservations made after the cut-off date or after the group room block has been filled (whichever comes first) will be accepted on a space- and rate- availability basis. Rooms are limited, so please book early. We understand that you have many choices when making your travel arrangements, and may ultimately decide to stay at another hotel. Please understand that reserving your room in the CHI room block allows you to take full advantage of the conference sessions, events and networking opportunities, and ensures that our staff will be available to help should you have any issues with your accommodations. Flight Discounts: Special discounts have been established with American Airlines for this conference: • Call American Airlines 800-433-1790 and use Conference code 7264AD. • Go to aa.com/group and enter Conference code 7264AD in promotion discount box. • Contact our designated travel agent, Rona Meizler, at 617-559-3735 or rona.meizler@protravelinc.com. Car Rental Discounts: Special rental discounts have been established with Hertz for this conference. • Call Hertz 800-654-3131 and use our Hertz Convention Number (CV): CV#04KL0005 • Go to hertz.com and use our Hertz Convention Number (CV): CV#04KL0005 information Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine
  • 9. ADDITIONAL REGISTRATION DETAILS Each registration includes all conference sessions, posters and exhibits, food functions, and access to the conference proceedings link. Handicapped Equal Access: In accordance with the ADA, Cambridge Healthtech Institute is pleased to arrange special accommodations for attendees with special needs. All requests for such assistance must be submitted in writing to CHI at least 30 days prior to the start of the meeting. To view our Substitutions/ Cancellations Policy, go to www.healthtech.com/regdetails Video and or audio recording of any kind is prohibited onsite at all CHI events. Complimentarynewsdeliveredtoyourinbox A series of diverse reports designed to keep life science professionals informed of the salient trends in pharmaceutical technology, business, clinical development, and therapeutic disease markets.For a detailed list of reports, visit InsightPharmaReports.com, or contact Rose LaRaia, rlaraia@healthtech.com, +1-781-972-5444. Barnett is a recognized leader in clinical education, training, and reference guides for life science professionals involved in the drug development process. For more information, visit barnettinternational.com. Cambridge Healthtech Associates™ (CHA™) leverages its extensive network and unique collaborative model in consulting, technology evaluations and community-based communication services to help clients in the life sciences industry commercialize and penetrate the marketplace to increase revenue. Visit www.chacorporate.com. SHORT COURSES Commercial Academic, Government, Hospital-affiliated One short course $699 $399 Three short courses BEST VALUE $999 $699 CONFERENCE PRICING (Includes access to 1 conference, excludes short courses) Advance Registration Discount until May 2, 2014 $2199 $1099 Registrations after May 2, 2014, and on-site $2399 $1149 CONFERENCE DISCOUNTS Poster Submission - Discount ($50 Off): Poster abstracts are due by May 2, 2014. Once your registration has been fully processed, we will send an email containing a unique link allowing you to submit your poster abstract. If you do not receive your link within 5 business days, please contact jring@healthtech.com. *CHI reserves the right to publish your poster title and abstract in various marketing materials and products. Alumni Discount SAVE 20%: Cambridge Healthtech Institute (CHI) appreciates your past participation at Clinical Genome Conference. As a result of the great loyalty you have shown us, we are pleased to extend to you the exclusive opportunity to save an additional 20% off the registration rate. Register 3 - 4th is Free! Individuals must register for the same conference or conference combination and submit completed registration form together for discount to apply. Alumni Discount and Register 3 and 4th is Free Discount cannot be combined. Group Discounts are Available! Special rates are available for multiple attendees from the same organization.For more information on group discounts contact David Cunningham at 781-972-5472 If you are unable to attend but would like to purchase the TCGC: The Clinical Genome Conference CD for $500 (plus shipping), please visit ClinicalGenomeConference.com. Massachusetts delivery will include sales tax. How to Register: ClinicalGenomeConference.com reg@healthtech.com • P: 781.972.5400 orToll-free in the U.S. 888.999.6288 Please use keycode CLG EF when registering Subscribe to New Bulletins or the Weekly Update Newsletter at Bio-ITWorld.com Clinical Trials to the Clinic, subscribe at ClinicalInformaticsNews.com Hotel Kabuki, San Francisco, CA June 10 - 12, 2014 CLINICALGENOMEconference THE 3rd ANNUAL Mining the Genome for Medicine Cover Agenda Sponsor & Exhibit Opportunities Hotel & Travel Information Short Courses Registration Information Click Here to Register Online! ClinicalGenomeConference.com Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 www.healthtech.com Mining the Genome for Medicine

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