Genetics and Genomics 2013

AUG 21 - 22 2013

Genetics and Genomics 2013

10679 45 132726

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The theme of this conference is a range of genetics and genomics topics such as RNAi, Next-generation sequencing, Cancer research, Sequencing, Genome-wide association studies GWAS, Epigenetics, Mapping, Exomes, Genomic medicine, Human Genome Structural Variation, Pharmacogenetics, DNA/RNA Purification, Mutations, Translational Genomics, Bioinformatics, Genotyping, Pharmacogenomics, Screening, Cloning, Gene Expression, Phenotyping, Transcription, Functional Genomics, Synthetic Biology, Genome Engineering, Immunology, qPCR/Real-Time PCR, PCR, Biomarkers, Stem Cell research, Human Identification, Bioproduction, Molecular Diagnostics and much more. Attendees can earn free CME and CEU Credits.

This event will bring together research scientists, post docs, principal investigators, lab directors and professionals from around the world to learn about recent advances in genetics and genomics. This conference offers an amazing opportunity as it is free to participants, and there will be no out-of-pocket expenses for travel. However, participants will still benefit from interacting with a global community of like-minded colleagues, without leaving the comfort of their office or home.

With the advent of genetic and genomic medicine, health care providers will benefit from attending this conference and gain knowledge including the understanding of genetic testing, how to calculate risk and when to refer a patient to a genetic specialist, how the application of genomics will be key to effective prevention and management of many of the most important health-care issues. They will learn skills including the ability to communicate genetic information, how to manage family dynamics, become up to date on tools that are available to help the health-care professionals convey complex genetic information to patients.

This program will help to convey to health care practitioners that genetics and genomics are qualitatively different from all other topics because it underlies all of pathophysiology, and is therefore the fundamental science of health and disease.

Conference participants will be able to:

Attend interactive live streaming video sessions
Have their questions answered in real-time by industry experts
Chat live with peers and speakers
Browse a virtual exhibit floor for solution providers
Earn free CME and CEU continuing educationn credits

No crowded airports, delayed flights or expensive hotel rooms, but still the look and feel of a first-rate conference with world renowned experts. Participants also benefit from the fact that experts and vendors are more accessible, no more waiting in line to speak to someone. Think it is too good to be true? Checkout the venue and become a believer.

Speakers:

Dave S Hoon, PhD

Chief of Scientific Intelligence, Director of Molecular Oncology, John Wayne Cancer Institute
Elaine Lyon, PhD

Associate Professor (Clinical) of Pathology, Division Medical Director, Genetics, Co-Program Director, Clinical Genetics Fellowship Program, Program Director, Molecular Genetics Fellowship Pr
Deanne Taylor, MS, PhD

Director Bioinformatics, Children's Hospital of Philadelphia, University of Pennsylvania
Cinnamon S Bloss, PhD

Director of Social Sciences & Bioethics, Assistant Professor, Scripps Translational Science Institute, Scripps Health & The Scripps Research Institute
Shawn Baker, PhD

CEO, CSO and Co-Founder, AllSeq, Inc.
Drew Endy, PhD

Assistant Professor of Bioengineering at Stanford, and President of The BioBricks Foundation
Anthony Marotta, PhD

Chief Scientific Officer, AugureX Life Sciences Corp
Kathryn E Wellen, PhD

Assistant Professor, Assistant Investigator, Abramson Family Cancer Research Institute, University of Pennsylvania Medicine
Thomas P Moyer, PhD

Professor of Laboratory Medicine, Mayo Clinic
Ivan Brukner, PhD

Head of Molecular Microbiology Unit- Molecular Biology, Jewish General Hospital - McGill University
Igor Grigoriev, PhD

Head, Fungal Genomics Program, US Department of Energy Joint Genome Institute
Bogi Eliasen, MSc

Program director for FarGen, Faroe Islands Ministry of Health
Matthew Keyser, MS

Senior Manager, NGS Applications, DNASTAR
David Baker, PhD

Investigator, Howard Hughes Medical Institute, Professor of Biochemistry, Adjunct Professor of Genome Sciences, Physics, Computer Science, Chemical Engineering, and Bioengineering, University
Patrick Tan, MD, PhD

Professor, Cancer & Stem Cell Biology Pgm, Duke-NUS Graduate Medical School Singapore, Sr. Group Leader, Genome Institute of Singapore, Program Leader, Genomic Oncology, Cancer Science In
Piero Carninci, PhD

Director, Division of Genomic Technologies, RIKEN Center for Life Science Technologies
Živana Težak, PhD

Associate Director for Science and Technology, Office of In Vitro Diagnostics and Radiological Health (OIR), CDRH, U.S. Food and Drug Administration
C Jimmy Lin, MD, PhD, MHS

Founder, President, CEO, TED Fellow, Rare Genomics Institute Washington University in St. Louis
John Quackenbush, PhD

Professor of Computational Biology and Bioinformatics, Department of Biostatistics, Harvard University, Dana-Farber Cancer Institute
Paul Billings, MD, PhD

Chief Medical Officer, Life Technologies
Noam Shomron, PhD

Principle Investigator, Genome Laboratory, Tel Aviv University
Kenneth Buetow, PhD, FACMI

Director of Computational Sciences and Informatics program for Complex Adaptive Systems and Professor in the School of Life Sciences, Arizona State University
Pinar Bayrak-Toydemir, MD, PhD

Associate Professor, Department of Pathology, University of Utah, Medical Director, Molecular Genetics and Genomics ARUP Laboratories
Howard J Jacob, PhD

Founding Director of the Personalized Medicine Program and Human and Molecular Genetics Center, Warren P. Knowles Chair of Genetics, Professor, Department of Physiology & Pediatrics, Medi
Edward Ki Yun Leung, PhD

Clinical Chemistry Postdoctoral Fellow, University of Chicago
John Mattick, PhD,AO, FAA, FRCPA

Executive Director, Garvan Institute of Medical Research, Conjoint Professor in the St Vincent's Hospital Clinical School and the Faculty of Medicine, at the University of New South Wale
Marcel Dinger, MSc (hons), PhD

Head of Clinical Genomics, Garvan Institute of Medical Research, Conjoint Associate Professor at the University of New South Wales
William C Nierman, PhD

Professor, Director, Infectious Diseases Program, J. Craig Venter Institute (JCVI)
Bruce R Korf, MD, PhD

Professor and Chair, Department of Genetics, Director, Heflin Center for Genomic Sciences, UAB
Michael F Berger, PhD

Assistant Professor in the Department of Pathology, Research Scientist, Memorial Sloan-Kettering Cancer Center
Michael Snyder, PhD

Professor and Chair, Genetics, Director, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine
Christopher I Amos, PhD

Associate Director for Population Sciences, Professor of Community and Family Medicine at the Geisel School of Medicine, Norris Cotton Cancer Center, Dartmouth College
Linnea Baudhuin, PhD, DABMG

Co-director, Pharmacogenomics and Genetics Laboratory, Co-director, Cardiovascular Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic
Matthew Lebo, PhD, FACMG

Instructor of Pathology, BWH and Harvard Medical School, Assistant Laboratory Director and Senior IS Domain Specialist Laboratory for Molecular Medicine, Partners HealthCare Center for Perso
George Church, PhD

Professor of Genetics, Director of the Center for Computational Genetics, Harvard Medical School
Andrew Hessel, MSc

Distinguished Research Scientist, Autodesk Inc., Faculty, Singularity University
Agnieszka Lichanska, PhD

Laboratory Director, TessArae, LLC
Alisa Jackson, Zach Smith, Mary Blair, Dave Delano

Alisa Jackson, Moderator, Beckman Coulter, Inc. Zach Smith, MS, Project Scientist, The Center for Genomics and Bioinformatics, Indiana University Mary Blair, Senior Application Scientist,
Charles Cantor, PhD

Chief Scientific Officer, Sequenom
Yaniv Erlich, PhD

Principal Investigator, Andria and Paul Heafy Family Fellow, MIT Whitehead Institute for Biomedical Research
Jessica C Mar, PhD

Assistant Professor, Department of Systems & Computational Biology, Assistant Professor, Department of Epidemiology & Population Health, Albert Einstein College of Medicine
Daniel Caffrey, PhD

Assistant Professor at the University of Massachusetts Medical School, Program Chair for the Bioinformatics Program, Instructor in the Rabb School of Continuing Studies, Division of Graduate
Steven Rosenberg, PhD

Chief Scientific Officer, CardioDx, Inc.
Patrice Milos, PhD

Chief Executive Officer, Claritas Genomics
Nir Barzilai, MD

Director, Institute for Aging Research, Ingeborg and Ira Leon Rennert Chair in Aging Research, Professor, Department of Medicine (Endocrinology), Professor, Department of Genetics, Albert Ein
Nathan R Treff, PhD

Director of Molecular BiologyResearch, Reproductive Medicine Associatesof New Jersey, Associate Professor, Department of Obstetrics, Gynecology,and Reproductive Sciences, UMDNJ-Robert Wood Jo
Bruce K Patterson, MD

CEO and Founder, IncellDx Inc
Vincent P Mauro, PhD

Associate Professor of Neurobiology, Scripps Institute
Kimberly Strong, PhD

Assistant Professor, Primary Faculty for the Program in Genomics and Ethics, Medical College of Wisconsin
Robert Roberts, MD, FRCPC, MACC, LLD (Hon.)

President, Chief Executive Officer and Chief Scientific Officer, Professor of Medicine, Director, Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute
David F Keren, MD

Professor, Department of Pathology, Associate Director, Clinical Pathology Laboratories, University of Michigan Health System

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All times are Pacific Time

AUG 21, 2013 06:00 AM PDT

M-protein Evaluation in an Age of Automation: Capillary Electrophoresis, Free Light Chains & Heavy-Light Measurements

Speaker: David F Keren, MD

This presentation focuses on contemporary methods for detection of monoclonal proteins (M-protiens) that are associated with multiple myeloma and other plasma cell dyscrasias. The basic principles of the techniques currently used will be presented along with a triage that can be used for their implementation. None of the techniques is without the hazards of false positive and false negative results. When using serum protein electrophoresis as the screen, the main causes for false positives include the presence of fibrinogen and genetic variants of normal serum proteins. When capillary electrophoresis is used to screen serum, radiocontrast dyes and some antibiotics can mimic M-proteins. False negatives occur because will be demonstrated along with tactics to prevent them. Serum free light chain testing is a boon to detecting multiple myeloma without requiring a 24 hour urine sample, however the user needs to be aware of the high-dose hook effect which can produce falsely low results. The newest serologic test is able to measure heavy and light chain specific pairs, i.e. distinguishing between populations of IgG kappa and IgG lambda. These reagents may aid in classification and risk stratification, but more independent research will be needed to determine their utility.

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AUG 21, 2013 06:00 AM PDT

What to use for targeted re-sequencing - microarrays or NGS?

Speaker: Agnieszka Lichanska, PhD

Genetic testing is becoming a widespread practice and with human genome fully sequenced we want to develop best methods to do it. Single gene or single mutation screening is pretty much becoming a thing of the past. Similarly using just single PCR for identifying mutations, while cheap and quick, is being slowly replaced by highly multiplex tests.Targeted re-sequencing applications analyze a subset of human genes and/or mutations and report back the sequence of fragments tested. Currently there are two technologies for doing that: sequencing by hybridization or Next Generation Sequencing. I will discuss the technical aspects, sample and analysis workflows, and validation protocols for re-sequencing assays. I will also briefly review some of the currently available assays for targeted re-sequencing highlighting their advantages, disadvantages and clinical use.

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AUG 21, 2013 06:00 AM PDT

You Can and Must Understand Synthetic Biology

Speaker: Andrew Hessel, MSc

A 2013 survey conducted by the Woodrow Wilson Synthetic Biology Project found that 75% of adults have heard just a little or nothing at all about synthetic biology, figures that were virtually unchanged since 2009. Meanwhile, the field, like DNA sequencing and systems biology before it, is growing in technological sophistication at a tremendous rate and disrupting conventional ideas and mechanisms in research, development, security and economics. It's like computers all over again, only in a different and more controversial medium ¬- life. This talk will introduce synthetic biology to a broad audience by comparing it to the evolution of computing and information technologies; describe key individuals, breakthroughs, and resources from recent years; and provide a future forward perspective based on trends and comparisons. By the the end of talk, the listener should feel a) confident that they have a basic understanding of synthetic biology; and b) some appreciation of the importance of the field to continued global technological and economic progress - if not the continued existence of the human species.

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AUG 21, 2013 07:00 AM PDT

Improving the Accuracy of Genome Sequencing and Interpretation

Speaker: George Church, PhD

Our ability to view and alter biology is progressing at an exponential pace -- faster even than electronics. Next generation sequencing can be used to assess inherited, environmental and epi- genomes. CLIA typically ensures reproducibility, but not necessarily highest accuracy. Genome sequence accuracy requires haplotype phase (measured, not merely inferred). Interpretation accuracy requires deep knowledge of the interactions of genomes, environments and traits. We can now move from mere correlation to causality by systematically synthesizing millions of genomic (and epi-genomic) variants via CRISPR technologies and human pluripotent stem cells. We test these technologies and interpretation software (http://GET-evidence.org ) using data and cells from the world's only fully shareable genomics resource (http://Personalgenomes.org) -- enabling clearer preview of precision medicine. The learning objectives of this session include measuring accuracy of the underlying data, the computational integration of diverse data types -- and informed consent in an era of leaks, rich data and re-identification.

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AUG 21, 2013 08:00 AM PDT

Clinical Applications in Pharmacogenetics

Speaker: Linnea Baudhuin, PhD, DABMG

As a component of individualized medicine, pharmacogenetics (PGx) focuses on how genetic factors influence individual responses to specific medications. The clinical goals of pharmacogenetics are to identify the right drug at the right dose for each patient. The majority of known PGx-related variability is due to variation in genes encoding drug metabolizing enzymes. Variable drug metabolism can result in adverse drug events, ineffective therapies, and noncompliance with therapy. Pharmacogenetic variability can also be due to genetic variation in genes encoding drug transporters, drug targets, and proteins involved in immune response. Drugs with known pharmacogenetic variability may be labeled with PGx-related information. One example is clopidogrel which was updated in March 2010 by the FDA to contain information regarding response to clopidogrel in cytochrome P450 2C19 (CYP2C19) poor metabolizers. It has been demonstrated that individuals with reduced function CYP2C19 alleles do not effectively convert clopidogrel to its active metabolite, and this is associated with an increased rate of subsequent cardiovascular events and death. Other examples of pharmacogenetic-related drug labeling include warfarin and CYP2C9 and VKORC1 variation, psychiatric medications and CYP2C19/CYP2C9/CYP2D6 variation, thiopurines and TPMT variation, hypersensitivy to carbamazepine and abacavir due to HLA-B variation, and irinotecan and UGT1A1 variation. These and other examples are the basis for different clinical applications in pharmacogenetics with the ultimate goal of utilizing genetic information to determine the appropriate drug and dose for each patient.

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AUG 21, 2013 08:00 AM PDT

Implementation of genome sequencing in a clinical diagnostic laboratory

Speaker: Matthew Lebo, PhD, FACMG

With the technical costs of genome sequencing continuously dropping, it is now feasible to offer this assay in a clinical context. Empirical evidence suggests that genome and exome sequencing may lead to a diagnosis in 25-30% of affected individuals, with even current costs of the sequencing being offset by savings in patient care management. Furthermore, the nature of the test allows for the identification of incidental findings in both affected and healthy individuals that may lead to further cost savings. In this talk, we'll detail the issues and complexities that arise from implementing genome sequencing as a clinical service, including methods and techniques to validate the assay and interpret the results. Furthermore we'll discuss approaches to create reports that return both results for the primary indication and for incidental findings, the former of which was used as the clinical report for the winning team of the recent CLARITY Challenge. We'll also detail our experiences offering genome sequencing in clinical care, including our support of the MedSeq project that is studying the return of patient genome sequence data to subspecialists and primary care physicians.

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AUG 21, 2013 08:00 AM PDT

Post Genome-Wide Association Studies

Speaker: Christopher I Amos, PhD

In this presentation I describe some of the approaches we are taking to identify the genetic architecture of common complex cancers with a particular focus on the etiology of lung cancer. Cancers results from joint effects of germline susceptibility along with common environmental exposures that propel risk for further stages of cancer development for some individuals. Genome-wide association studies have been highly effective in providing new insights into the etiology of these cancers. For lung cancer, genome-wide association analysis identified a key region of chromosome 15q that contains variants of nicotinic acetyl choline receptors that are expressed at low levels in most of the brain except a few selected areas, so these were not considered as primary candidates for smoking behavior nor for lung cancer risk. Further study of these loci shows they play a key role in lung cancer development as well as in tobacco use and smoking cessation. In particular, individuals with high risk variants have particular difficulty in tobacco cessation unless provided with pharmacological support. Other findings from genetic analysis of lung cancer have shown dramatic heterogeneity by histological subtype. A region on chromosome 5p21 harboring hTERT and CLPTM1L shows heterogeneity by histology, but animal models show that CLPTM1L plays a role in cancer progression. Finally, we discuss the role of sequencing for understanding the genetic architecture of cancers and how the limited resources available for genetic analysis might be applied for both sequencing and genome-wide assessment.

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AUG 21, 2013 09:00 AM PDT

Adventures in Personal Genomics and Whole Omics Profiling

Speaker: Michael Snyder, PhD

Personalized medicine is expected to benefit from the combination of genomic information with the global monitoring of molecular components and physiological states. To ascertain whether this can be achieved, we determined the whole genome sequence of an individual at high accuracy and performed an integrated Personal Omics Profiling (iPOP) analysis, combining genomic, transcriptomic, proteomic, metabolomic, and autoantibodyomic information, over a 38-month period that included healthy and two virally infected states. Our iPOP analysis of blood components revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways across healthy and disease conditions. Importantly, genomic information was also used to estimate medical risks, including Type 2 Diabetes, whose onset was observed during the course of our study. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.

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AUG 21, 2013 10:00 AM PDT

Azole resistance in Aspergillus fumigatus - clinical isolate screening, culture selection, and genetics

Speaker: William C Nierman, PhD

In the United States, invasive aspergillosis (IA), an invasive fungal infection of the upper respiratory tract of immune compromised patients, is usually caused by Aspergilus fumigatus, while Aspergillus flavus represents only a small fraction of IA cases. In some countries A. flavus is the most frequent IA pathogen. Recently, we described a novel, highly virulent, aggressively invasive, and drug resistant IA pathogen, Aspergillus tanneri. In mouse models of IA and in a non-vertebrate insect model we observed distinct virulence profiles for the three Aspergillus species. Comparative genomics showed that A. tanneri had a larger genome than the other Aspergilli, encoding nearly 1900 more genes than A. fumigatus. A. tanneri genes had numerous orthologs in the other two genomes, however an abundance of genes are unique to A. tanneri. Among the unique genes were multiple gene clusters that encode biosynthetic genes for the synthesis of secondary metabolites, suggesting that A. tanneri produces novel secondary metabolites that may play a role in its high level of pathogenicity. Analysis of genes commonly associated with drug resistance showed that A. tanneri carried CYP51A mutations resulting in or contributing to azole resistance. An important issue featured in the A. tanneri fatal cases and in clinical management of IA is the general limitation in treatment options - only four classes of drugs are available in the context of ever-increasing drug resistance. Drugs used to treat fungal infections target only two differences between human and fungal cells: the presence of ergosterol in fungal cell membranes and of glucans in their cell walls. There remains an urgent need to understand the broad range of genes encoded in the genomes of fungal pathogens that participate in the resistance to the clinically therapeutic antifungals employed in treating infections. To identify novel mechanisms that mediate azole resistance in A. fumigatus, we used whole genome sequencing of in vitro selected azole-resistant strains. To further refine the most significant mechanisms required for resistance, we developed a genetic-sexual system that enables the analysis of complex traits in A. fumigatus and revealed that at least 6 mechanisms for azole resistance exist in this organism. These include mutations in the target protein, CYP51A, and in an additional co-target HMG CoA reductase. The results from this study identify novel drug targets in A. fumigatus and also show that next-generation sequencing coupled with classical genetics experiments is a powerful way to identify genes involved in complex traits.

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AUG 21, 2013 10:00 AM PDT

Genomic Approaches to Discover Biomarkers of Drug Response in Cancer

Speaker: Michael F Berger, PhD

Massively parallel sequencing technology has proven to enable the identification of driver genetic alterations in patients' tumors that may be suppressed by targeted therapies. Through retrospective analysis of clinical specimens, one can discover genomic biomarkers that predict outcomes and therapeutic response. Longitudinal profiling of multiple tumors in a single patient can reveal factors that influence tumor progression and drug resistance. Finally, prospective sequencing of patient specimens, when coupled with complementary radiology and histology based imaging, can enhance the clinical diagnosis and treatment of cancer patients. For increasingly lower costs, one can profile clinically relevant genes for mutations, copy number alterations, and structural rearrangements, with high detection sensitivity in low purity or multi-clonal tumor tissue. Advances in target capture, sample multiplexing, and profiling of formalin-fixed paraffin embedded (FFPE) specimens have further established the clinical utility of next generation sequencing. However, challenges remain in the application of these techniques to the analysis of clinical samples. In addition to the technical challenge of analyzing scant amounts of FFPE tissue, one must overcome the biological challenges of aneuploidy and heterogeneity inherent to the genetics of cancer. I will discuss different strategies for sequencing clinical samples, including different sequencing platforms, capture methods, and breadth of testing (i.e. targeted versus comprehensive approaches). I will describe examples in which our group has performed massively parallel sequencing on clinically annotated tumor specimens to identify genomic biomarkers of drug response and resistance. Finally, I will describe additional challenges in prospectively applying these techniques for clinical diagnosis involving bioinformatics, clinical interpretation, regulatory compliance, and ethics.

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AUG 21, 2013 10:00 AM PDT

Integration of Genomics into Medical Practice: Educational Challenges

Speaker: Bruce R Korf, MD, PhD

Medical applications of genetics and genomics have been advancing dramatically since completion of the sequencing of the human genome. The cost of DNA sequencing has plummeted, leading to the rapid introduction of sequencing-based testing into the clinic. Genomics has already changed our approach to prevention, diagnosis, and treatment of disease; the day is not far off when most medical decisions will be to some extent informed by the outcome of a genetic or genomic test. Most practicing physicians were trained well prior to the genomic era, and even those who remember what they were taught about genetics will find that the field has changed beyond recognition. Although some of the genomics applications will be mediated through point-of-care decision support systems, there is a need for physicians to gain competency in multiple areas of genetic and genomic medicine. This includes use and interpretation of genetic and genomic predictive and diagnostic tests, using pharmacogenetic information to adjust drug administration, and customizing treatment to specific subtypes of disease defined by genetic testing. Physicians will also need to be able to incorporate the results of genome sequencing, including responding to incidental findings of genetic changes that indicate risk of disease. These educational challenges will need to be met for physicians in training and in practice, and will require the use of multiple educational modalities, including use of approaches such as online courses and case studies. Genetics and genomics may also be built into the maintenance of certification requirements in many specialty areas. There is a great need for innovative approaches to genetics and genomics education that will prepare physicians and other health providers, recognizing the increasing complexity of medical care generally and the increasing demands on the time of all practitioners.

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AUG 21, 2013 11:00 AM PDT

Panel Discussion: Meeting the Demand of Increased NGS Capacity with Automated TruSeq Stranded mRNA Library Preparation

Speaker: Alisa Jackson, Zach Smith, Mary Blair, Dave Delano

RNASeq has become the primary method for studying changes in gene expression in modern genomics research. By directly sequencing the various types of RNA molecules, including mRNA, ncRNA, and small RNA, researchers can build an accurate profile of gene expression under various conditions, allowing the elucidation of gene function and regulation. RNASeq has been further refined recently with the development of stranded RNASeq, which modifies the existing RNASeq library construction methodology to preserve information regarding which DNA strand the RNA transcript originated from. Among other advantages, stranded RNASeq allows for more accurate mapping of RNASeq transcripts to reference genomes, which in turn results in a more accurate view of the transcriptome. Increasingly, researchers are designing more complex experiments involving population level transcriptomic surveys and time course studies, both of which require high throughput RNASeq library construction methods that consistently generate high quality RNASeq libraries. In response, we developed an automated RNASeq library construction method using the Beckman Coulter Biomek FXP liquid handling system in conjunction with TruSeq Stranded mRNA library preparation chemistry from Illumina. By combining Illumina's proven chemistry with the highly efficient Biomek FXP liquid handling system, we have developed a flexible library construction protocol that allows for the creation of up to 96 individually indexed Illumina stranded mRNA libraries by a single technician over the course of approximately 8.5 hours of machine time.

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AUG 21, 2013 12:00 PM PDT

Genetics of Coronary Artery Disease

Speaker: Robert Roberts, MD, FRCPC, MACC, LLD (Hon.)

Susceptibility to coronary artery disease (CAD) is claimed to be 40% to 60% inherited, but until recently genetic risk factors predisposing to CAD have been elusive. Comprehensive prevention of CAD requires manipulation of genetic risk. The availability of microarrays of single-nucleotide polymorphisms enabling genome-wide association studies (GWAS) led to the discovery of 50 genetic risk variants for CAD. Surprisingly, 35 risk variants mediate their risk through unknown mechanisms, with only 17 associating with hypertension or lipids. Thus, there are several mechanisms contributing to the pathogenesis of CAD yet to be elucidated. The first risk variant discovered by GWAS was 9p21.3, which occurs in 75% of all populations except African, with a mean increased risk of 25% per copy. Of the 50 variants for CAD, the increased risk varies from 6% to 92% with a mean increased risk of 18%, occurring on average in 47% of the population. The maximum number of risk alleles per individual would be 100. In the CARDIoGRAM (Coronary Artery Disease Genome-wide Replication and Meta Analysis) study of 23 variants, the average per individual was 17, the minimum 7, and the maximum 37. The top 10th percentile has an odds ratio of 1.88 and the lowest percentile an odds ratio of 0.55. Routine genetic screening is unlikely until management is improved by genetic testing. Risk variants should provide pathophysiological insights and targets for novel therapy. While risk variants are less potent predictors of CAD, compared with biomarkers, they have the advantage of not changing in one's lifetime and are unaffected by diet, sex, age, or medication.

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AUG 21, 2013 12:00 PM PDT

Genome Hacking

Speaker: Yaniv Erlich, PhD

Sharing sequencing datasets without identifiers has become a common practice in genomics. We recently showed that some datasets can be fully re-identified by using entirely free, publicly accessible Internet resources. I will present quantitative analysis about the probability of identifying US individuals by this technique on hundreds of genetic datasets. In addition, I will demonstrate the power of our approach by tracing back the identities of multiple whole genome datasets in public sequencing repositories.

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AUG 21, 2013 12:00 PM PDT

Noninvasive Cancer Genomics

Speaker: Charles Cantor, PhD

Whenever there is cell death, apoptotic cell free DNA fragments appear in the circulation of the host. These fragments, typically 145-160 base pairs in size, represent a minute fraction of total DNA in the host circulation. If care is taken to avoid host cell breakage, the apoptotic DNA fragments can be analyzed to provide information about the genome of the cells that produced them. In pregnancy, analysis of apoptotic DNA fragments has allowed the development of very effective noninvasive aneuploidy testing. Indeed it is possible to reconstruct the entire fetal genomic DNA sequence from these fragments. In cancer it is possible to view copy number, sequence, and epigenetic differences between the tumor and the host by analyzing circulating free DNA. While this work is still at early stages it is reasonable to predict that an array of useful noninvasive cancer diagnostic tests should soon result from such studies. It is furthermore likely that a careful search for informative apoptotic DNA fragments that differ in methylation from DNA in the circulation of a normal host might lead to methods for the early detection of other clinical situations that are characterized by inappropriate cell death.

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AUG 21, 2013 01:00 PM PDT

Bioinformatics and Quantitative Genomics in Cervical Cancer Screening

Speaker: Bruce K Patterson, MD

Cervical cancer screening has evolved significantly since the PAP smear was introduced in 1949. In particular, the association with human papillomavirus (HPV) infection and the mechanism of HPV-related carcinogenesis have been elucidated over the last 20 years. Diagnostics quickly followed focusing on the presence or absence of HPV. Because HPV is ubiquitous and the presence of a high risk type of HPV results in high grade cervical lesions in a small number of instances, the field has realized that infection by HPV is not enough to appropriately triage affected individuals into treatment categories. Detection of HPV DNA has high sensitivity (95%+) for high grade cervical lesions but low specificity (

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AUG 21, 2013 01:00 PM PDT

Codon optimization: new safety concerns for gene therapy and genetic vaccines

Speaker: Vincent P Mauro, PhD

Codon-optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. It is used extensively for expressing recombinant protein drugs, gene therapy, and DNA/RNA vaccines. However, it is becoming increasingly clear that codon-optimization can affect protein conformation and function, increase the immunogenicity of recombinant protein drugs, and reduce efficacy. This presentation will analyze the mechanisms and assumptions underlying codon optimization and identify additional hazards associated with this approach, including unique hazards for gene therapy and DNA/RNA vaccine applications.

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AUG 21, 2013 01:00 PM PDT

In sickness and in health: variables effecting genome sequencing ethical issues

Speaker: Kimberly Strong, PhD

In addition to the exciting promise that genome sequencing holds, concerns are also often described. These concerns relate to: privacy/confidentiality of findings; impact of findings on insurability and discrimination; autonomy and the impact of one's findings on others; questions of clinical utility; the potential for psychological distress; and equity of access. While each of these concerns may constitute a reason for some not to pursue sequencing technology at this time, others remain ready and willing to move forward immediately. Clearly the weighing of risks and benefits are different for different people. Delineating these differences will take time and require empirical exploration. One seemingly obvious bot often neglected differentiation is the starting point for individuals (or family members) - whether they are sick or healthy. Decision making in the context of illness likely (and understandably) influences the weightings given to risks and benefits - perhaps even reframing the balance of promise and concern entirely (a "game changer"). This talk will present the various concerns put forward regarding genome sequencing and discuss the ways in which these are more and/or less relevant depending upon one's relative health situation.

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AUG 21, 2013 02:00 PM PDT

Claritas Genomics: The Future of Pediatric Diagnostics is Now

Speaker: Patrice Milos, PhD

Increasingly genome sequence knowledge is unraveling the complexity of rare Mendelian disorders offering hope for our children's medical care through better disease diagnosis and ultimately patient care. When combined with the emerging new sequencing technologies, allowing large scale genome analysis to move rapidly into clinical laboratories, new opportunities arise for more precise medical care. Claritas Genomics was founded to deliver on the promise of science and technology merging for medical care. Our presentation will discuss the current needs for molecular diagnostics in pediatric populations and provide a better understanding of the role Claritas plays in enabling better patient decisions. Founded as a genetic diagnostic testing company, Claritas combine the power of next-generation DNA sequencing technology with the clinical expertise of the world's best pediatric specialists to assist in informing and improving patient care. Claritas offers a full range to support physician test ordering and support needed as they care for patients, navigating an increasingly complex landscape of genetic diagnostics. Our genomic interpretive services are based on the most up to date and reliable scientific findings and our reports are designed to clearly communicate this complex genetic information. Originally Boston Children's Hospital's CLIA molecular testing laboratory, and launched as an independent CLIA/GLP laboratory in February 2013, we have an existing comprehensive menu of tests, with new next-generation sequencing-based services to be launched in the fall of 2013. Through our partnership with Life Technologies, Claritas is also well positioned to offer cutting edge advances in DNA sequencing, offering products from single gene tests through to whole exomes. Claritas also maintains a close relationship with Boston Children's and its renowned investigators, to uniquely position us to translate novel research-based discoveries into diagnostic clinical practice. Thus we aim to enable health care providers to integrate genomics into the future of their routine medical practice responsibly and Claritas takes pride in our partnership with both our ordering clinicians and the genetic researchers making discoveries that will lead to new tests and clinical knowledge.

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AUG 21, 2013 02:00 PM PDT

Comprehensive Chromosome Screening in the Human Embryo

Speaker: Nathan R Treff, PhD

The human species is particularly prone to chromosome segregation errors during maternal meiosis in the egg and during post zygotic mitosis in the preimplantation embryo. In fact, aneuploidy represents the most common genetic abnormality in humans, and is the primary cause of infertility, affecting 1 in 6 couples. Despite the extremely limited amount of DNA available from a human embryo, development of genetic technologies, such as qPCR and next generation sequencing, now allow accurate and effective analysis of the copy number of all 24 chromosomes in preimplantation stage human embryos produced during in vitro fertilization (IVF). Selection of chromosomally normal embryos improves the efficacy of single embryo transfer, eliminating the primary complication of IVF (multiple gestations), and improves the success of treating infertility. This presentation will detail the development, validation, and future directions of new human embryo comprehensive chromosome screening technologies.

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AUG 21, 2013 02:00 PM PDT

The role of protective genes in the exceptional longevity of humans

Speaker: Nir Barzilai, MD

Aging is the major risk for diseases such as cancer, AD, type 2 Diabetes mellitus and cardiovascular disease. We hypothesize that a progress in preventing these diseases will occur only if we can understand the reason people age at different rates, and develop strategy to delay aging. Certainly the environment plays a major role in our aging, and environmental intervention, such as caloric restriction, can delay aging significantly in many biological models. While we can measure biological changes with aging we cannot assume they are the cause. In fact the challenge is to determine which changes may be the cause/s of aging and which are protective mechanisms against the changes that occurs. One approach to understand aging is to study the oldest old people who are relatively healthy. We established such a unique cohort of individuals with exceptional longevity (~600 Ashkenazi Jews ages 95-112) and their offspring (approximate age 70 years) and age- and sex-matched controls without a family history of unusual longevity. This matched group of offspring of exceptional longevity-proband and their controls are a powerful tool for identifying genetically controlled longevity traits.

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AUG 21, 2013 03:00 PM PDT

Discovery, Development, and Clinical Validation of Gene Expression Scores for Transplant Rejection and Coronary Artery Disease

Speaker: Steven Rosenberg, PhD

Introduction Although the focus of the genomics community has largely been on DNA polymorphisms which affect disease risk, gene expression, especially of blood cells, has the potential to reflect genetic and environmental factors and to inform on both current and future disease status. The immune system dysregulation underlying many human diseases, including transplant rejection, and coronary artery disease (CAD), coupled with development of global blood gene expression profiling and quantitative RT-PCR, has enabled the clinical use of blood-based gene expression tests. Methods Blood samples were obtained from heart transplant or coronary disease patients and paired with results from gold standards of pathologist core-lab read endomyocardial biopsies (EMB) or quantitative coronary angiographic analysis on invasive angiograms, respectively. Discovery, development and validation steps were used to identify genes, develop algorithms, and validate algorithm performance with pre-specified statistical and clinical analysis plans. Development and validation cohorts were obtained in prospective multi-center trials. Finally, the performance and impact of these tests on usual care was assessed in observational or interventional studies. Results For heart transplant rejection largely independent cohorts were used to discover and develop an 11 gene algorithm to discriminate high-grade rejection from quiescence. In a set of independent patient blood samples the ROC curve AUC was 0.72; subsequent comparison of this algorithm with EMB in a prospective interventional trial met the primary endpoint of non-inferiority with a significant reduction in EMB. For CAD diagnosis, after gene discovery by microarrays, independent cohorts from a multi-center angiographic study were used to develop and validate a 23-gene whole blood RT-PCR based algorithm to discriminate obstructive CAD, with a second validation study assessing performance in patients referred for myocardial perfusion imaging. ROC AUC in these two validation studies were 0.70 and 0.79, respectively. Conclusions Blood-based gene expression tests have been developed and are being using clinically.

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AUG 21, 2013 03:00 PM PDT

Evolution of Alu elements in long non-coding RNA and mRNA

Speaker: Daniel Caffrey, PhD

Long non-coding RNAs (lncRNA) are a novel class of RNA molecule that are emerging as important regulators of gene transcription and post-transcriptional events. lncRNAs have been shown to regulate a broad variety of biological processes and are often located within regions of the genome that are associated with various diseases. Repetitive elements are a major component of lncRNA and their molecular functions in lncRNA are poorly understood. Here, I describe the evolution of Alu elements in lncRNA and mRNA. Alu elements are the most abundant transposable element in the human genome (more than 1 million copies) and their composition and evolution within lncRNA and mRNA differ significantly. These striking differences are correlated with their expression and suggest a common molecular function in lncRNA and mRNA.

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AUG 21, 2013 03:00 PM PDT

Investigating tissue specificity of cancer-causing germline mutations

Speaker: Jessica C Mar, PhD

The remarkable diversity we see between different cell types in the human body is governed by the specificity attained through transcriptional and epigenetic regulatory programs. Cancer is a disease that targets specific tissues, and in the case of cancer-causing germline mutations, it is perplexing that primary tumors arise in a restricted subset of tissues only. Understanding why a mutation can be suppressed in one tissue but not others stands to unlock insights into tissue-specific transcriptional regulation and how these programs promote fragility or resistance of cancer-causing mutations. We have been studying cancer-causing germline mutations in the context of cell type-specific gene regulatory networks. Using a comprehensive tissue expression atlas from the FANTOM5 consortium, we have access to CAGE sequencing data that captures promoter usage and gene expression in over 1000 human samples, including primary cells, tissues and cell lines. Levering information from COSMIC, the Cancer Gene Census, and FANTOM5, two classes of genes that have tissues-specific, cancer-causing mutations have been identified - (1) genes that are expressed in the cell type where the cancer occurs, (2) genes that are expressed ubiquitously across many different cell types. For this second class, we have begun comparing regulatory networks associated with these genes in susceptible versus resistant cell types to identify changes in network topology that may change a cell type's oncogenic potential.

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AUG 21, 2013 04:00 PM PDT

Development of Targeted Next Generation Sequencing for Pharmacogenomics

Speaker: Edward Ki Yun Leung, PhD

The goal of personalized medicine is to customize healthcare to the individual patient. Pharmacogenomics, the analysis of how a patient's genetic makeup affects the individual's response to certain drugs, plays a major role in the realization of personalized medicine. Pharmacogenomics studies the influence of genetic variation on the patient's drug response by correlating single-nucleotide polymorphisms (SNPs) with the drug's efficacy and/or toxicity, and therefore with the hope of optimizing drug therapy with respect to the patent's genotype, to ensure maximum efficacy with minimal adverse effects. Currently, most pharmacogenomic studies have been done using DNA chip arrays. A large amount of genetic information is generated in a cost effective way when using DNA chip arrays. However, one limitation of using this technology is that only a subset of mutations are analyzed and different manufacturers may use different SNPs to identify the same haplotype. Recent technological developments with next-generation sequencing (NGS) have enabled pharmacogenomics analysis at costs approaching to the cost of using DNA chip arrays. The advantage of using NGS is that all the SNPs corresponding to a haplotype can be analyzed. Currently, there are only a few targeting-sequencing kits for pharmacogenomics are commercially available. Because these kits may not cover some SNPs of interest, custom sequencing panels are needed to ensure that all interested SNPs are covered. This presentation will go over some of the important features of some commonly used targeted-enrichment technologies for NGS that are desirable for pharmacogenomic studies. This presentation will also highlight some of the challenges of developing and implementing pharmacogenomic NGS in a clinical laboratory for routine patient sample analysis.

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AUG 21, 2013 04:00 PM PDT

Lighting up the dark matter of the genome: Unravelling the roles of noncoding DNA in disease and development

Speaker: Marcel Dinger, MSc (hons), PhD

Approximately 98% of the human genome comprises noncoding DNA, the function of which is largely unknown. Intriguingly, more than 85% of single nucleotide polymorphisms identified to be associated with disease in genome-wide studies (GWAS) occur within noncoding regions, suggesting that examining the role of these regions of the genome will be important for understanding and potentially treating disease. The relatively recent discovery of widespread transcription of potentially functional long noncoding RNAs (lncRNAs) from the mammalian genome led us to investigate whether or not GWAS hits in noncoding regions could be reconciled by the transcription of regulatory RNAs from these loci. LncRNAs typically show highly developmental-stage- and tissue-specific expression, and therefore cannot be easily detected by conventional RNA-Seq, which requires exponentially greater depth to detect increasingly rare transcripts. To overcome this problem, we developed a technique termed RNA-Capture-Seq, which combines custom capture tiling arrays with RNA sequencing to target transcription arising from specific areas of the genome. We have used this approach to target 300 chromosomal regions identified by GWAS. Using RNA from diverse human tissues, we identify thousands of novel transcripts associated with the majority of the targeted regions. To further realise the potential of the method to understand specific diseases, we have designed further capture arrays to target GWAS regions linked to specific diseases. For these experiments, RNA from biologically relevant normal and disease tissues were used to look for novel transcripts. As a result, we have identified numerous new lncRNAs whose expression appears to be specifically associated with disease and arise from disease-associated regions. Although functional investigation of these transcripts is still underway, we propose that the results of these experiments bring an intriguing new perspective into our understanding of how information in the genome is encoded and has considerable potential to identify novel regulators, which may prove valuable as biomarkers and therapeutic targets, involved in disease and development.

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AUG 21, 2013 04:00 PM PDT

The hidden layer of RNA regulation in human development

Speaker: John Mattick, PhD,AO, FAA, FRCPA

High throughput transcriptomic analyses have shown that most of the human genome is dynamically transcribed to produce an extraordinary range of overlapping and interlacing intronic, intergenic and antisense RNAs, many of which are alternatively spliced, to produce a previously hidden universe of long and short regulatory RNAs. These RNAs fulfill various functions in gene expression, with miRNAs and related species being best (although not well) understood. The functions of the long noncoding RNAs (lncRNAs), which range from hundreds to hundreds of thousands of bases in length, are varied and include central roles in the formation of various differentiation-specific subnuclear organelles. However, recent evidence suggests that the major function of lncRNAs is to guide chromatin-modifying complexes to their sites of action, to specify the architectural trajectories of development and differentiation. In addition, it appears that these RNAs are subject to context-dependent editing, particularly in the brain, which appears to be, along with transposon mobility, the molecular basis of physiological and cognitive plasticity. The transcriptome is in fact far more complex than the genome, which is best viewed as a zip file that is unpacked in highly cell-specific patterns during development. Focused RNA sequencing (using oligonucleotide capture to target specific loci, similar to exome sequencing) reveals thousands of previously unknown exons and spliced isoforms of oncogenes and tumor suppressors, as well as a rich landscape of lncRNAs expressed from genomic regions, including GWAS regions associated with complex diseases, that superficially appear to be transcriptionally bare by conventional deep sequencing. Not surprisingly, it is also emerging that variations in the sequence or expression of these RNAs not only underpin phenotypic differences between individuals and species, but also play significant roles in the etiology of complex diseases, including as cancer and neurological diseases.

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AUG 21, 2013 05:00 PM PDT

Fungal Genomics for Energy and Environment

Speaker: Igor Grigoriev, PhD

There are over 1.5 Million fungal species and they play critical role in shaping Earth ecosystems. Better understanding of pathogens and symbionts is critical for a sustainable growth of plants. Fungi are the most efficient degraders of plant biomass to convert it into bioenergy. Many other new metabolic processes and enzymes are encoded in fungal genomes. Fungal genomics may offer answers to critical challenges of future such as food, medicine, energy and the environment. This talk will describe approaches used in large scale genomics- to explore phylogenetic and ecological diversity of fungi. It will also illustrated how genomic data can improve our understanding of plant-fungal interactions and enable practical applications for energy and the environment.

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AUG 21, 2013 05:00 PM PDT

Global penetration of genomic-like techniques into fast clinical diagnostics of infective diseases in emergency: applicability and technological bottle-necks?

Speaker: Ivan Brukner, PhD

Dr Ivan Brukner entered into genomic era back in 1989 (ex-Yugoslavia), trying to describe and solve repeating sequence "branching motif problem" in building whole genome sequence. Next 5-10 years, his research was targeting sequence-dependent DNA structural problems, where contradictory puzzle about origin of DNA curvature and bending (crystallographic versus soft biochemistry data) was resolved (Italy, Germany and Canada). In 2000-2007, focus was directed toward design of nucleic-acid-based "ideal" point of care diagnostic device. Robust, multiplex, hybridization-based diagnostic device (which operates at standard "room" temperatures - in spite of ~90% sequence cross-similarity) was constructed and functionally tested. The universal protocol for selection of "robust" hybridization probes was result of this adventure. After joining Jewish General Hospital in Montreal (~2009), his work was becoming more clinically applicable, focusing on high volume molecular assays with strong financial and/or diagnostic impact (MRSA, C.difficile, VRE). He realized the strong need for applicability of new molecular techniques in emergency, including NGS, and definition of technological bottlenecks is subject of his talk in this secession.

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AUG 22, 2013 07:00 AM PDT

Metabolic reprogramming: links to the epigenome

Speaker: Kathryn E Wellen, PhD

Cancer cells are characterized by major alterations in both cellular metabolism and epigenetic profiles. Current understanding of links between metabolism and chromatin in the context of cancer is currently very limited. We have previously demonstrated that acetylation of histones is sensitive to glucose availability through the enzyme ATP-citrate lyase (ACL), which produces acetyl-CoA from citrate. While this is likely to impact gene expression and other chromatin-dependent processes, the molecular mechanisms and functional significance of metabolic regulation of lysine acetylation are poorly understood. In this presentation, I will focus on current efforts to elucidate how metabolic signals are conveyed to chromatin. I will also discuss recent findings demonstrating a novel link between ACL and another chromatin-modifying enzyme, DNA methyltransferase 1, during adipocyte differentiation.

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AUG 22, 2013 07:00 AM PDT

Soluble 14-3-3? - A Personalised Rheumatoid Arthritis Patient Management Strategy

Speaker: Anthony Marotta, PhD

Rheumatoid Arthritis (RA) is a heterogenous disease that affects 1.5% of the population. Similar to cancer, early detection coupled with an effective treatment strategy can significantly improve patient outcomes. In the advent of new classes of RA therapies, there is an impetus to identify new serological markers that mark risk of RA development, prognosis and therapy response. 14-3-3 eta (?) is a new RA marker that is available for clinical use in the US through Quest Diagnostics. 14-3-3? is one of 7 members of the 14-3-3 family and is specifically present in the serum of patients with RA and erosive psoriatic arthritis (PsA). In the healthy state, these proteins reside within the intracellular space governing various biological processes including proliferation, differentiation and metabolism. Increased expression of different 14-3-3 isoforms correspond with worse prognosis in certain cancers and neurological disorders. In RA, the 14-3-3? protein is specifically externalized and can be measured in serum, making it a useful clinical serum marker. When 14-3-3? exists in the extracellular environment, it behaves as a soluble ligand inducing factors that drive inflammation and joint damage also making it a novel therapeutic target. This presentation will describe the discovery of 14-3-3? in arthritis, its development pathway and the biomarker's clinical utility. We will discuss how the 14-3-3? biomarker pipeline has evolved from the protein R&D programs into a 14-3-3? biomarker suite that serves as a direct companion to a first-in-class RA personalized medicine drug target.

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AUG 22, 2013 07:00 AM PDT

Warfarin Sensitivity Testing

Speaker: Thomas P Moyer, PhD

Anticoagulation therapy is frequently employed to prevent stroke in patients with atrial fibrillation, prophylaxis of venous thromboembolism and pulmonary embolism in patients with prosthetic heart valves and myocardial infarction, and prevention of pulmonary embolism or deep vein thrombosis after orthopedic surgery or with a history of venous or arterial thromboembolism. Warfarin is an effective anticoagulant that can be prescribed for prolonged periods of time. However, warfarin causes adverse events; if under-dosed, clots may form causing stroke, and if overdosed, life-threatening bleeding may occur. Rivaroxaban and dabigatrin have recently come on the market as warfarin alternatives. While these drugs are reported to produce fewer adverse events, clinical experience suggests otherwise; adverse events do occur. More importantly, there are no reversal agents for these new drugs; managing an anticoagulant induced bleed by one of these agents is difficult. Pharmacogenomic (PG) testing has been applied to warfarin to reveal genetic variants that predict warfarin adverse events. The liver enzyme Cytochrome P450 2C9 metabolizes warfarin. Three variants have been extensively studied; these variants decrease warfarin metabolism predisposing patients to warfarin overdose. The enzyme Vitamin K Epoxide Reductase, known as VKORC1, converts Vitamin K to the reduced form required to activate clotting factors II, VII, IX, and X. Genetic variants in VKORC1 decrease enzyme activity causing warfarin to induce a more profound decrease in activated clotting factors than normal. Patients with this variant are more likely to experience warfarin-induced bleeding. Application of PG testing to large patient populations suggests that modified warfarin dosing based on results of PG reduce warfarin adverse events by more than 35%; this makes warfarin essentially equivalent to rivaroxaban in terms of efficacy. Summing the benefits of 50 plus years clinical experience with warfarin, availability of a reversal agent for warfarin-induced bleeding, and availability of PG testing to guide dosing, warfarin may be the safest anticoagulant on the market today.

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AUG 22, 2013 08:00 AM PDT

Aliens, Computers & Engineering Biology - An Introduction to Synthetic Biology

Speaker: Drew Endy, PhD

Synthesis and assembly of DNA powerfully enables reverse genetics-based approaches to scientific discovery. I'll present recent and unpublished work on genome refactoring and redesign, focusing on identification of cryptic genetic elements and genome decompression. Next, I'll summarize work published over the past year in which we reported the first non-volatile and rewritable digital genetic data storage systems, amplifying genetic logic gates, and programmed cell-cell communication via arbitrary DNA messages. These experiences will be used to frame ten years of research in synthetic biology, by which the foundational engineering ideas of abstraction and standardization have finally been shown as not impossible to make true, and that when made true enable our designer DNA systems to work reliably the first time.

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AUG 22, 2013 09:00 AM PDT

Management and Analysis of Pre-implantation Genetic Diagnosis Data

Speaker: Deanne Taylor, MS, PhD

During IVF procedures pre-implantation genetic diagnosis (PGD) allows for genetic profiling of embryos prior to replacement. Most PGD procedures during IVF are performed to select chromosomally normal embryos as comprehensive chromosome screening (CCS), and in a smaller number of cases PGD is used for embryo selection against known genetic disease variants carried by the parents. Genomic technologies utilizing PCR, microarray, and second-generation sequencing methods are currently being used for PGD data analysis in the laboratory. With decreasing costs in second-generation sequencing technologies coupled with increased demand for PGD, adoption of "PGD-seq" methods for CCS and genetic selection will face significant future challenges in data management, analysis and information delivery to clinicians. One of our goals is to provide secure, integrated environments for clinicians to use genetic information to inform treatment strategies. I discuss challenges and strategies for storing and integrating biomedical data with other private and public data repositories. I discuss process and warehouse design, analysis methods and implementation strategies for PGD and genetics data. I discuss how we deliver and visualize PGD data for clinicians and to researchers in clinical and basic science.

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AUG 22, 2013 09:00 AM PDT

Next-Gen Sequencing: Driving the Transition from Genetics to Genomics

Speaker: Shawn Baker, PhD

The rapid advancements in next generation sequencing have served the research market very well, delivering more and more sequence for less and less money. While these advancements are still being made, the market is now looking toward serving a new customer - the clinician. For both technology platforms and informatics solutions, the emphasis is now on speed, quality and ease of use. An understanding of this market and where it is headed will help in predicting the broad implications for the future of medicine.

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AUG 22, 2013 09:00 AM PDT

Return of Genome Sequencing Results to Physicians and Patients

Speaker: Cinnamon S Bloss, PhD

There has been considerable debate in the scientific and clinical communities regarding the return of results from genome sequencing to physicians and patients. Questions surrounding which health care professional(s) should deliver this information, as well as what types of results should be returned loom large. The aim of the Scripps Idiopathic Diseases of huMan (IDIOM) study is to use genome sequencing to inform diagnosis and treatment of idiopathic diseases. As part of this study, we assess patient and provider preferences surrounding the types of results returned from sequencing, as well as perceptions of the return-of-results communication itself. This is done via semi-structured interviews and standardized questionnaires. Data collected to date suggest that the majority of probands and their parents would prefer, if given the choice, to receive sequencing results for the presenting condition, as well as secondary findings in multiple disease categories (e.g., actionable and non-actionable, childhood and adult-onset). Further, data from the completed return-of-results sessions suggest notable variation in patient satisfaction with communication of results by the referring physician. This includes, in some cases, a marked discrepancy between the extent to which the physician felt results were communicated effectively versus the extent to which the patient perceived the communication to be effective. These case-by-case findings will be discussed in detail. Through the Scripps IDIOM study we have begun collection of empirical data on patient preferences and perceptions regarding return of results from genome sequencing for diagnosis and treatment of idiopathic disease. It is our hope that these data will help inform the development of an effective, sustainable, and cost-effective model of return of individual results from genome sequencing in clinical settings.There has been considerable debate in the scientific and clinical communities regarding the return of results from genome sequencing to physicians and patients. Questions surrounding which health care professional(s) should deliver this information, as well as what types of results should be returned loom large. The aim of the Scripps Idiopathic Diseases of huMan (IDIOM) study is to use genome sequencing to inform diagnosis and treatment of idiopathic diseases. As part of this study, we assess patient and provider preferences surrounding the types of results returned from sequencing, as well as perceptions of the return-of-results communication itself. This is done via semi-structured interviews and standardized questionnaires. Data collected to date suggest that the majority of probands and their parents would prefer, if given the choice, to receive sequencing results for the presenting condition, as well as secondary findings in multiple disease categories (e.g., actionable and non-actionable, childhood and adult-onset). Further, data from the completed return-of-results sessions suggest notable variation in patient satisfaction with communication of results by the referring physician. This includes, in some cases, a marked discrepancy between the extent to which the physician felt results were communicated effectively versus the extent to which the patient perceived the communication to be effective. These case-by-case findings will be discussed in detail. Through the Scripps IDIOM study we have begun collection of empirical data on patient preferences and perceptions regarding return of results from genome sequencing for diagnosis and treatment of idiopathic disease. It is our hope that these data will help inform the development of an effective, sustainable, and cost-effective model of return of individual results from genome sequencing in clinical settings.

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AUG 22, 2013 10:00 AM PDT

Clinical Interpretation of Sequence Variants

Speaker: Elaine Lyon, PhD

The advent of massively parallel sequencing by next generation sequencing platforms now allow genomic approaches for individualizing healthcare. Genomic sequencing data reveals variants in genes related to drug metabolism that may affect efficacy or response. This presentation will describe the potential of NGS data for companion diagnostics or therapeutics and its implementation into clinical laboratories. Evaluating pharmacogenetic targets through exome analysis as well as through targeted gene panels will be discussed.

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AUG 22, 2013 10:00 AM PDT

FarGen - a holistic genomic health approach

Speaker: Bogi Eliasen, MSc

The FarGen project aims to sequence the whole genome of the entire Faroese population. Together with existing genetic records, such a comprehensive sequencing project can significantly improve treatment and prevention services in the Faroese public health system. The project has also great potential in an international research context as it can contribute significantly to our general understanding of human genetics. An understanding of genetics has proved crucial in health systems of the future, and genetic studies are already being used in Faroese health system. And with the introduction of the Human Genetics Act and the Genetic Biobank in 2006, the stage was set for a thriving genetic research environment in the Faroe Islands. The digitalisation of the Faroese genome, combined with the extensive health records in the Faroese health system, will significantly boost our general understanding of health issues, resulting in improved treatment and prevention services in the Faroe Islands. Thanks to our coherent health system, our special legislation (the Human Genetics Act), our digital public health register, and not least our digitalised genealogy records, the FarGen project has attracted a great deal of interest from international researchers. With these unique features, the Faroe Islands may well the ideal place for incorporating genetic research into the public health system. Both education and the ELSI play a significant role in a nationwide project like the FarGen and parallel to the sequencing a educational system for both health staff, school and the general public is been developed.

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AUG 22, 2013 10:00 AM PDT

Using Prostate Cancer Exome Data to Identify Candidate Genes

Speaker: Matthew Keyser, MS

In this presentation, exome data from individuals with prostate cancer will be aligned against an annotated reference human genome and SNPs will be identified using DNASTARs SeqMan NGen software. SNPs and associated genes from disease samples will be compared against numerous control samples and a list of genes known to be implicated in prostate cancer or other cancers to identify additional candidate SNPs and genes in sample data. All work will be done using DNASTARs Lasergene Genomics Suite software, which is available on desktop computers or on the Amazon Cloud. The integration of these capabilities within one software package facilitates fast, comprehensive analysis, helping researchers move quickly from raw next-generation sequence data to informative results.

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AUG 22, 2013 11:00 AM PDT

Design of protein structures, functions and assemblies

Speaker: David Baker, PhD

I will describe recent advances in computational protein design which allow the generation of new protein structures and functions. I will describe the use of these methods to design ultra-stable idealized proteins, flu neutralizing proteins, high affinity ligand binding proteins, and self assembling protein nanomaterials. I will discuss possible applications to therapeutics, vaccines and diagnostics. I will also describe the contributions of the general public to these efforts through the distributed computing project Rosetta@home and the online protein folding and design game FoldIt.

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AUG 22, 2013 12:00 PM PDT

Exome Sequencing as a Diagnostic Tool

Speaker: Pinar Bayrak-Toydemir, MD, PhD

It is widely accepted that approximately 85% of known disease-causing DNA variants affect the exons and splice junctions, which is about 1% of the whole genome. As a result, Clinical Exome Sequencing is a powerful and highly efficient diagnostic tool to identify disease-causing DNA variants in individuals. In this talk, I will discuss the methodology, validation, reporting, and bioinformatics aspects of clinical exome sequencing. In addition, I will talk about the regulations regarding reporting of incidental findings and the American College of Medical Genetics guidelines. I will include discussion of advantages and disadvantages of the methodology based on examples of positive and negative clinical exome sequencing results.

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AUG 22, 2013 12:00 PM PDT

Use of Whole Genome Sequencing in Clinical Practice

Speaker: Howard J Jacob, PhD

Howard J. Jacob, Ph.D., Founding Director of the Personalized Medicine Program and Human and Molecular Genetics Center and Professor in Physiology and Pediatrics at the Medical College of Wisconsin and Children's Hospital of Wisconsin. In 2010 Dr. Jacob led a team of researchers at the Medical College who for the first time ever were able to use the human genome to diagnose and treat a young boy, Nicholas Volker whose life threatening disease had baffled his doctors. Nik is now leading a fully and healthy life. Dr. Jacob completed his Ph.D. at the University of Iowa followed by fellowships at MIT, Harvard and Stanford. He has published over 230 papers. He is an entrepreneur and serves on several scientific advisory boards.

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AUG 22, 2013 01:00 PM PDT

Dominant regulation of gene expression by microRNAs

Speaker: Noam Shomron, PhD

MicroRNAs are short non-coding cellular regulators of gene expression. Each microRNA controls the expression of a large set of genes, and microRNAs collectively, may regulate more than half of human genes. In the laboratory, our team focuses on understanding the function of microRNAs in health and during disease. We map their expression in developing cancer cells and in various brain disorders. We predict direct gene targets of these microRNAs sets and then pinpoint the cellular pathways affected. I will present our recent findings in the field and discuss its potential implications for prognosis and diagnosis. Overall our team pursues research that aims to deepen our understanding on the development of diseases in order to generate a significant impact through translating ideas into clinical reality.

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AUG 22, 2013 01:00 PM PDT

Embracing the Complexity of Cancer: Seeing the Forest and the Trees

Speaker: Kenneth Buetow, PhD, FACMI

Personalized medicine is transforming biomedical research and healthcare service delivery. Disease definition, diagnosis, treatment, and prevention are being fundamentally altered by the capacity to routinely perform comprehensive molecular characterization. Nowhere is this change happening faster than in the field of cancer. Increasingly sophisticated technology provides the capacity to describe, in multiple molecular dimensions, the tumor and the individual in which it has developed. These technologies identify the millions of variants present in normal individuals and thousands of alterations that occur during the course of the disease process. This systems-wide molecular analysis of constitutional and somatic tissues has identified a complex cacophony of inherited and acquired variation. Coherence emerges from these data when evaluated using biologic networks as analytic frameworks. These networks account for the individual heterogeneity in underlying etiology as well as the diversity of events necessary to generate a complex phenotype such as cancer. Emerging collections of analytic approaches permit analysis using genome-wide data sets and established biologic networks as models. The generation of this unprecedented amount of data presents us with the challenge contextualizing that data and converting into actionable information. The integration and interpretation of this complex multidimensional information into the evidence necessary to support clinical care exceeds the raw human cognitive capacity. Information systems have the capacity to provide the needed "tool" to tackle this challenge - to generate the necessary evidence to support the delivery of personalized medicine. Arizona State University's (ASU) Complex Adaptive Systems team is building such an Evidence Engine in its Next Generation Cyber Capability (NGCC). The ASU NGCC - composed of networks, hardware, software, and people transforms "Big Data" to information and creates the evidence necessary to enable personalized medicine.

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AUG 22, 2013 02:00 PM PDT

The Road to Genomic Medicine is Paved with Data and Information

Speaker: John Quackenbush, PhD

Since the introduction of second-generation DNS sequencing technologies in 2007, the cost of genome sequencing has been consistently by 33% per quarter, with the $1000 genome arriving in 2012 and the $100 genome not far off. As DNA sequencing increasingly becomes a commodity, biomedical research is rapidly evolving from a purely laboratory science to an information science in which the winners in the race to cure disease are likely to be those best able to collect, manage, analyze, and interpret data. Here I will provide an overview of the approach we have been developing to deal with the challenge of personal genomic data, including integrative approaches to data analysis and the creation of data portals focused on addressing the most common use cases presented by different user constituencies. By effectively collecting genomic and clinical data and linking information available in the public domain, we have made significant advances in uncovering the cellular networks and pathways that underlie human disease and building predictive models of those networks that may help to direct therapies.

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AUG 22, 2013 02:00 PM PDT

Translation and Clinical Application of Innovative Genomic Analysis: Challenges Remain

Speaker: Paul Billings, MD, PhD

The role of the human genome in normal and patho-biology is crucial. Applied in cancer care and in a variety of unknown disorder settings, it can provide key insights and crucial diagnostic/prognostic/predictive/other information. Its methods can also help improve clinical practices already provided. But many challenges remain that could delay its beneficial application, increase errors, or add unnecessary costs. In this talk, I will review the field of clinical genomic analysis generally and then focus on important challenges in its translation and clinical applications.

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AUG 22, 2013 03:00 PM PDT

Evaluation challenges and regulatory considerations for next-generation sequencing and other high throughput genomic technology based clinical applications

Speaker: Živana Težak, PhD

The use of ultrahigh throughput diagnostic tests that determine genetic sequence variation to guide patient care is rapidly expanding, fueled by the enormous growth in sequencing platform development. With the emergence of novel technologies, the FDA is faced with new regulatory challenges while continuing to apply scientific evidence-based oversight. While there are no broadly accepted standards or methods to analytically validate ultrahigh throughput sequencing tests yet, there are a number of efforts underway, including establishing reference materials to aid in assessing analytical performance. The additional challenge in informed clinical application of sequence information is inadequate knowledge about correlations between genomic variations and their clinical significance. The FDA is proactively working to encourage cross-collaboration in this area. Ultimately, the FDA has to balance public safety concerns with fostering innovation and enabling the translation of emerging technologies that can improve medical care and benefit public health.

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AUG 22, 2013 03:00 PM PDT

Next-generation Cancer Care in the Age of Genomics, Precision Medicine, High Throughput Biology

Speaker: C Jimmy Lin, MD, PhD, MHS

Developments in DNA sequencing technology have provided a unique opportunity for diagnosis and discovery of genetic alterations for rare diseases. Partnering with 20 academic centers in the US and globally, we have coordinated and facilitated NGS projects for rare disease. We will summarize what we learned from all these sites for the entire process from consent, sample collection, library prep, sequencing, bioinformatics, interpretation, counseling, and clinical reimbursement.

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AUG 22, 2013 04:00 PM PDT

Complexity of Mammalian Transcription

Speaker: Piero Carninci, PhD

The next generation sequencing technologies are profoundly influencing our way to study biology. We have previously developed cap-analysis gene expression (CAGE) to simultaneously mRNA/noncoding RNA starting sites and simultaneously detect their expression. Altogether, CAGE achieves comprehensive coverage of transcription starting site and allows to assign newly discovered promoters/5' ends to the rest of the RNA sequence (CAGEscan technology). With these technologies, we can infer the transcriptional networks that regulate gene expression. This technology is being applied to a broad range of samples to elucidate the promotome and the regulatory networks of mouse and human primary cells and tissues in the FANTOM5 project. DeepCAGE allows also detecting dynamic expression of repeat elements, which show peculiar expression patterns and provide alternative promoters and functional genome elements. We have also used deepCAGE on subcellular fractions as a part of the ENCODE project. We have detected clear patterns of expression of retrotransposon elements (RE) in a panel of human and mouse tissues, which are likely to have a regulatory role. Now, we have clearly identified specific patterns of non-coding RNAs and other RE-derived RNA in different cell compartments, with a particular interesting role of LINE elements, which seem to be preferentially bound to the chromatin. Other retrotransposon elements, like LTRs, are prevalently expressed in ES and iPS cells, where they may have a role to keep the stem cells undifferentiated. Altogether, these data are pointing at a potential function of the retrotransposon elements and other ncRNAs to regulate the epigenome.

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AUG 22, 2013 05:00 PM PDT

Clinical Utility Potential of Epigenetic Aberrations in Human Solid Tumors

Speaker: Dave S Hoon, PhD

As Chief of Scientific Intelligence at the John Wayne Cancer Institute, Dr. Hoon interacts with external academic, industry, and government agencies to develop innovative translational research opportunities. He has coauthored more than 250 peer-reviewed articles and reviews, primarily related to translational molecular oncology of human solid tumors. He has over 25 patents on his studies. As founding Director of the Department of Molecular Oncology, Dr. Hoon continues to pioneer investigations of RNA/genomic/epigenomic biomarkers for diagnostic, prognostic and predictive assessment of residual tumor cells. He also spearheads investigations of circulating DNA/miRNA biomarkers for staging cancer in patients enrolled in phase II/III clinical trials. The Department's focus on biomarker expression in both tissue and body-fluid specimens gives it a uniquely broad scope. Dr. Hoon's team has developed diagnostic tissue biomarkers for molecular staging of sentinel lymph nodes and classification of human solid tumors such as melanoma, breast cancer and gastrointestinal cancer. Dr. Hoon also has pioneered development of blood-based nucleic-acid and tumor-cell biomarkers as prognostic tools. In the last decade he and his team have designed and conducted biomarker companion studies as part of multicenter international clinical trials. On the therapeutic front, Dr. Hoon is examining functional genomic and epigenomic changes as potential targets for development of novel approaches to treat or prevent malignancy. Dr. Hoon and the Department are funded by the National Institutes of Health/National Cancer Institute, the California Breast Cancer Research Program, Susan G. Komen for the Cure, Adelson Melanoma Research Foundation, the United States Department of Defense, and the pharma-biotech industry. Dr. Hoon has served on several review study sections as a permanent member for the National Cancer Institute, and was a founding member of NCI's Cancer Biomarker Study Section. The Department of Molecular Oncology consists of over 20 MD/PhD scientists and research technicians focused on translation molecular oncology. Some of the major ongoing collaborations include: Leiden University Medical Center, Netherlands; Genome Institute Singapore, Biopolis; Broad Institute of MIT and Harvard; Keio University; MD Anderson, and Melanoma Institute Australia. Dr. Hoon has trained more than 60 postdoctoral oncology fellows, who now hold faculty appointments in numerous academic institutions.

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AUG 22, 2013 05:00 PM PDT

Genomic Profiles of Asian Endemic Cancers

Speaker: Patrick Tan, MD, PhD

Malignancies caused by so-called Type I chemical and biological carcinogens provide important opportunities studying early events in cancer development, providing essential information for developing future cancer prevention strategies. In Asia, several highly lethal cancers are known to be caused by pathogens, such as stomach cancers (H. pylori), bile duct cancers (liver flukes), and certain lymphoma subtypes (Epstein-Barr Virus). For many of these conditions, treatment options are still highly limited. In this talk, I will describe how genomic analysis of infection-related Asian cancers can provide insights into cellular processes disrupted by these pathogens, and how such data can be used to identify new therapeutic targets.

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AUG 21, 2013 06:00 AM PDT

M-protein Evaluation in an Age of Automation: Capillary Electrophoresis, Free Light Chains & Heavy-Light Measurements

Speaker: David F Keren, MD

This presentation focuses on contemporary methods for detection of monoclonal proteins (M-protiens) that are associated with multiple myeloma and other plasma cell dyscrasias. The basic principles of the techniques currently used will be presented along with a triage that can be used for their implementation. None of the techniques is without the hazards of false positive and false negative results. When using serum protein electrophoresis as the screen, the main causes for false positives include the presence of fibrinogen and genetic variants of normal serum proteins. When capillary electrophoresis is used to screen serum, radiocontrast dyes and some antibiotics can mimic M-proteins. False negatives occur because will be demonstrated along with tactics to prevent them. Serum free light chain testing is a boon to detecting multiple myeloma without requiring a 24 hour urine sample, however the user needs to be aware of the high-dose hook effect which can produce falsely low results. The newest serologic test is able to measure heavy and light chain specific pairs, i.e. distinguishing between populations of IgG kappa and IgG lambda. These reagents may aid in classification and risk stratification, but more independent research will be needed to determine their utility.

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AUG 21, 2013 06:00 AM PDT

What to use for targeted re-sequencing - microarrays or NGS?

Speaker: Agnieszka Lichanska, PhD

Genetic testing is becoming a widespread practice and with human genome fully sequenced we want to develop best methods to do it. Single gene or single mutation screening is pretty much becoming a thing of the past. Similarly using just single PCR for identifying mutations, while cheap and quick, is being slowly replaced by highly multiplex tests.Targeted re-sequencing applications analyze a subset of human genes and/or mutations and report back the sequence of fragments tested. Currently there are two technologies for doing that: sequencing by hybridization or Next Generation Sequencing. I will discuss the technical aspects, sample and analysis workflows, and validation protocols for re-sequencing assays. I will also briefly review some of the currently available assays for targeted re-sequencing highlighting their advantages, disadvantages and clinical use.

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AUG 21, 2013 06:00 AM PDT

You Can and Must Understand Synthetic Biology

Speaker: Andrew Hessel, MSc

A 2013 survey conducted by the Woodrow Wilson Synthetic Biology Project found that 75% of adults have heard just a little or nothing at all about synthetic biology, figures that were virtually unchanged since 2009. Meanwhile, the field, like DNA sequencing and systems biology before it, is growing in technological sophistication at a tremendous rate and disrupting conventional ideas and mechanisms in research, development, security and economics. It's like computers all over again, only in a different and more controversial medium ¬- life. This talk will introduce synthetic biology to a broad audience by comparing it to the evolution of computing and information technologies; describe key individuals, breakthroughs, and resources from recent years; and provide a future forward perspective based on trends and comparisons. By the the end of talk, the listener should feel a) confident that they have a basic understanding of synthetic biology; and b) some appreciation of the importance of the field to continued global technological and economic progress - if not the continued existence of the human species.

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AUG 21, 2013 07:00 AM PDT

Improving the Accuracy of Genome Sequencing and Interpretation

Speaker: George Church, PhD

Our ability to view and alter biology is progressing at an exponential pace -- faster even than electronics. Next generation sequencing can be used to assess inherited, environmental and epi- genomes. CLIA typically ensures reproducibility, but not necessarily highest accuracy. Genome sequence accuracy requires haplotype phase (measured, not merely inferred). Interpretation accuracy requires deep knowledge of the interactions of genomes, environments and traits. We can now move from mere correlation to causality by systematically synthesizing millions of genomic (and epi-genomic) variants via CRISPR technologies and human pluripotent stem cells. We test these technologies and interpretation software (http://GET-evidence.org ) using data and cells from the world's only fully shareable genomics resource (http://Personalgenomes.org) -- enabling clearer preview of precision medicine. The learning objectives of this session include measuring accuracy of the underlying data, the computational integration of diverse data types -- and informed consent in an era of leaks, rich data and re-identification.

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AUG 21, 2013 08:00 AM PDT

Clinical Applications in Pharmacogenetics

Speaker: Linnea Baudhuin, PhD, DABMG

As a component of individualized medicine, pharmacogenetics (PGx) focuses on how genetic factors influence individual responses to specific medications. The clinical goals of pharmacogenetics are to identify the right drug at the right dose for each patient. The majority of known PGx-related variability is due to variation in genes encoding drug metabolizing enzymes. Variable drug metabolism can result in adverse drug events, ineffective therapies, and noncompliance with therapy. Pharmacogenetic variability can also be due to genetic variation in genes encoding drug transporters, drug targets, and proteins involved in immune response. Drugs with known pharmacogenetic variability may be labeled with PGx-related information. One example is clopidogrel which was updated in March 2010 by the FDA to contain information regarding response to clopidogrel in cytochrome P450 2C19 (CYP2C19) poor metabolizers. It has been demonstrated that individuals with reduced function CYP2C19 alleles do not effectively convert clopidogrel to its active metabolite, and this is associated with an increased rate of subsequent cardiovascular events and death. Other examples of pharmacogenetic-related drug labeling include warfarin and CYP2C9 and VKORC1 variation, psychiatric medications and CYP2C19/CYP2C9/CYP2D6 variation, thiopurines and TPMT variation, hypersensitivy to carbamazepine and abacavir due to HLA-B variation, and irinotecan and UGT1A1 variation. These and other examples are the basis for different clinical applications in pharmacogenetics with the ultimate goal of utilizing genetic information to determine the appropriate drug and dose for each patient.

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AUG 21, 2013 08:00 AM PDT

Implementation of genome sequencing in a clinical diagnostic laboratory

Speaker: Matthew Lebo, PhD, FACMG

With the technical costs of genome sequencing continuously dropping, it is now feasible to offer this assay in a clinical context. Empirical evidence suggests that genome and exome sequencing may lead to a diagnosis in 25-30% of affected individuals, with even current costs of the sequencing being offset by savings in patient care management. Furthermore, the nature of the test allows for the identification of incidental findings in both affected and healthy individuals that may lead to further cost savings. In this talk, we'll detail the issues and complexities that arise from implementing genome sequencing as a clinical service, including methods and techniques to validate the assay and interpret the results. Furthermore we'll discuss approaches to create reports that return both results for the primary indication and for incidental findings, the former of which was used as the clinical report for the winning team of the recent CLARITY Challenge. We'll also detail our experiences offering genome sequencing in clinical care, including our support of the MedSeq project that is studying the return of patient genome sequence data to subspecialists and primary care physicians.

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AUG 21, 2013 08:00 AM PDT

Post Genome-Wide Association Studies

Speaker: Christopher I Amos, PhD

In this presentation I describe some of the approaches we are taking to identify the genetic architecture of common complex cancers with a particular focus on the etiology of lung cancer. Cancers results from joint effects of germline susceptibility along with common environmental exposures that propel risk for further stages of cancer development for some individuals. Genome-wide association studies have been highly effective in providing new insights into the etiology of these cancers. For lung cancer, genome-wide association analysis identified a key region of chromosome 15q that contains variants of nicotinic acetyl choline receptors that are expressed at low levels in most of the brain except a few selected areas, so these were not considered as primary candidates for smoking behavior nor for lung cancer risk. Further study of these loci shows they play a key role in lung cancer development as well as in tobacco use and smoking cessation. In particular, individuals with high risk variants have particular difficulty in tobacco cessation unless provided with pharmacological support. Other findings from genetic analysis of lung cancer have shown dramatic heterogeneity by histological subtype. A region on chromosome 5p21 harboring hTERT and CLPTM1L shows heterogeneity by histology, but animal models show that CLPTM1L plays a role in cancer progression. Finally, we discuss the role of sequencing for understanding the genetic architecture of cancers and how the limited resources available for genetic analysis might be applied for both sequencing and genome-wide assessment.

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AUG 21, 2013 09:00 AM PDT

Adventures in Personal Genomics and Whole Omics Profiling

Speaker: Michael Snyder, PhD

Personalized medicine is expected to benefit from the combination of genomic information with the global monitoring of molecular components and physiological states. To ascertain whether this can be achieved, we determined the whole genome sequence of an individual at high accuracy and performed an integrated Personal Omics Profiling (iPOP) analysis, combining genomic, transcriptomic, proteomic, metabolomic, and autoantibodyomic information, over a 38-month period that included healthy and two virally infected states. Our iPOP analysis of blood components revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways across healthy and disease conditions. Importantly, genomic information was also used to estimate medical risks, including Type 2 Diabetes, whose onset was observed during the course of our study. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.

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AUG 21, 2013 10:00 AM PDT

Azole resistance in Aspergillus fumigatus - clinical isolate screening, culture selection, and genetics

Speaker: William C Nierman, PhD

In the United States, invasive aspergillosis (IA), an invasive fungal infection of the upper respiratory tract of immune compromised patients, is usually caused by Aspergilus fumigatus, while Aspergillus flavus represents only a small fraction of IA cases. In some countries A. flavus is the most frequent IA pathogen. Recently, we described a novel, highly virulent, aggressively invasive, and drug resistant IA pathogen, Aspergillus tanneri. In mouse models of IA and in a non-vertebrate insect model we observed distinct virulence profiles for the three Aspergillus species. Comparative genomics showed that A. tanneri had a larger genome than the other Aspergilli, encoding nearly 1900 more genes than A. fumigatus. A. tanneri genes had numerous orthologs in the other two genomes, however an abundance of genes are unique to A. tanneri. Among the unique genes were multiple gene clusters that encode biosynthetic genes for the synthesis of secondary metabolites, suggesting that A. tanneri produces novel secondary metabolites that may play a role in its high level of pathogenicity. Analysis of genes commonly associated with drug resistance showed that A. tanneri carried CYP51A mutations resulting in or contributing to azole resistance. An important issue featured in the A. tanneri fatal cases and in clinical management of IA is the general limitation in treatment options - only four classes of drugs are available in the context of ever-increasing drug resistance. Drugs used to treat fungal infections target only two differences between human and fungal cells: the presence of ergosterol in fungal cell membranes and of glucans in their cell walls. There remains an urgent need to understand the broad range of genes encoded in the genomes of fungal pathogens that participate in the resistance to the clinically therapeutic antifungals employed in treating infections. To identify novel mechanisms that mediate azole resistance in A. fumigatus, we used whole genome sequencing of in vitro selected azole-resistant strains. To further refine the most significant mechanisms required for resistance, we developed a genetic-sexual system that enables the analysis of complex traits in A. fumigatus and revealed that at least 6 mechanisms for azole resistance exist in this organism. These include mutations in the target protein, CYP51A, and in an additional co-target HMG CoA reductase. The results from this study identify novel drug targets in A. fumigatus and also show that next-generation sequencing coupled with classical genetics experiments is a powerful way to identify genes involved in complex traits.

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AUG 21, 2013 10:00 AM PDT

Genomic Approaches to Discover Biomarkers of Drug Response in Cancer

Speaker: Michael F Berger, PhD

Massively parallel sequencing technology has proven to enable the identification of driver genetic alterations in patients' tumors that may be suppressed by targeted therapies. Through retrospective analysis of clinical specimens, one can discover genomic biomarkers that predict outcomes and therapeutic response. Longitudinal profiling of multiple tumors in a single patient can reveal factors that influence tumor progression and drug resistance. Finally, prospective sequencing of patient specimens, when coupled with complementary radiology and histology based imaging, can enhance the clinical diagnosis and treatment of cancer patients. For increasingly lower costs, one can profile clinically relevant genes for mutations, copy number alterations, and structural rearrangements, with high detection sensitivity in low purity or multi-clonal tumor tissue. Advances in target capture, sample multiplexing, and profiling of formalin-fixed paraffin embedded (FFPE) specimens have further established the clinical utility of next generation sequencing. However, challenges remain in the application of these techniques to the analysis of clinical samples. In addition to the technical challenge of analyzing scant amounts of FFPE tissue, one must overcome the biological challenges of aneuploidy and heterogeneity inherent to the genetics of cancer. I will discuss different strategies for sequencing clinical samples, including different sequencing platforms, capture methods, and breadth of testing (i.e. targeted versus comprehensive approaches). I will describe examples in which our group has performed massively parallel sequencing on clinically annotated tumor specimens to identify genomic biomarkers of drug response and resistance. Finally, I will describe additional challenges in prospectively applying these techniques for clinical diagnosis involving bioinformatics, clinical interpretation, regulatory compliance, and ethics.

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AUG 21, 2013 10:00 AM PDT

Integration of Genomics into Medical Practice: Educational Challenges

Speaker: Bruce R Korf, MD, PhD

Medical applications of genetics and genomics have been advancing dramatically since completion of the sequencing of the human genome. The cost of DNA sequencing has plummeted, leading to the rapid introduction of sequencing-based testing into the clinic. Genomics has already changed our approach to prevention, diagnosis, and treatment of disease; the day is not far off when most medical decisions will be to some extent informed by the outcome of a genetic or genomic test. Most practicing physicians were trained well prior to the genomic era, and even those who remember what they were taught about genetics will find that the field has changed beyond recognition. Although some of the genomics applications will be mediated through point-of-care decision support systems, there is a need for physicians to gain competency in multiple areas of genetic and genomic medicine. This includes use and interpretation of genetic and genomic predictive and diagnostic tests, using pharmacogenetic information to adjust drug administration, and customizing treatment to specific subtypes of disease defined by genetic testing. Physicians will also need to be able to incorporate the results of genome sequencing, including responding to incidental findings of genetic changes that indicate risk of disease. These educational challenges will need to be met for physicians in training and in practice, and will require the use of multiple educational modalities, including use of approaches such as online courses and case studies. Genetics and genomics may also be built into the maintenance of certification requirements in many specialty areas. There is a great need for innovative approaches to genetics and genomics education that will prepare physicians and other health providers, recognizing the increasing complexity of medical care generally and the increasing demands on the time of all practitioners.

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AUG 21, 2013 11:00 AM PDT

Panel Discussion: Meeting the Demand of Increased NGS Capacity with Automated TruSeq Stranded mRNA Library Preparation

Speaker: Alisa Jackson, Zach Smith, Mary Blair, Dave Delano

RNASeq has become the primary method for studying changes in gene expression in modern genomics research. By directly sequencing the various types of RNA molecules, including mRNA, ncRNA, and small RNA, researchers can build an accurate profile of gene expression under various conditions, allowing the elucidation of gene function and regulation. RNASeq has been further refined recently with the development of stranded RNASeq, which modifies the existing RNASeq library construction methodology to preserve information regarding which DNA strand the RNA transcript originated from. Among other advantages, stranded RNASeq allows for more accurate mapping of RNASeq transcripts to reference genomes, which in turn results in a more accurate view of the transcriptome. Increasingly, researchers are designing more complex experiments involving population level transcriptomic surveys and time course studies, both of which require high throughput RNASeq library construction methods that consistently generate high quality RNASeq libraries. In response, we developed an automated RNASeq library construction method using the Beckman Coulter Biomek FXP liquid handling system in conjunction with TruSeq Stranded mRNA library preparation chemistry from Illumina. By combining Illumina's proven chemistry with the highly efficient Biomek FXP liquid handling system, we have developed a flexible library construction protocol that allows for the creation of up to 96 individually indexed Illumina stranded mRNA libraries by a single technician over the course of approximately 8.5 hours of machine time.

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AUG 21, 2013 12:00 PM PDT

Genetics of Coronary Artery Disease

Speaker: Robert Roberts, MD, FRCPC, MACC, LLD (Hon.)

Susceptibility to coronary artery disease (CAD) is claimed to be 40% to 60% inherited, but until recently genetic risk factors predisposing to CAD have been elusive. Comprehensive prevention of CAD requires manipulation of genetic risk. The availability of microarrays of single-nucleotide polymorphisms enabling genome-wide association studies (GWAS) led to the discovery of 50 genetic risk variants for CAD. Surprisingly, 35 risk variants mediate their risk through unknown mechanisms, with only 17 associating with hypertension or lipids. Thus, there are several mechanisms contributing to the pathogenesis of CAD yet to be elucidated. The first risk variant discovered by GWAS was 9p21.3, which occurs in 75% of all populations except African, with a mean increased risk of 25% per copy. Of the 50 variants for CAD, the increased risk varies from 6% to 92% with a mean increased risk of 18%, occurring on average in 47% of the population. The maximum number of risk alleles per individual would be 100. In the CARDIoGRAM (Coronary Artery Disease Genome-wide Replication and Meta Analysis) study of 23 variants, the average per individual was 17, the minimum 7, and the maximum 37. The top 10th percentile has an odds ratio of 1.88 and the lowest percentile an odds ratio of 0.55. Routine genetic screening is unlikely until management is improved by genetic testing. Risk variants should provide pathophysiological insights and targets for novel therapy. While risk variants are less potent predictors of CAD, compared with biomarkers, they have the advantage of not changing in one's lifetime and are unaffected by diet, sex, age, or medication.

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AUG 21, 2013 12:00 PM PDT

Genome Hacking

Speaker: Yaniv Erlich, PhD

Sharing sequencing datasets without identifiers has become a common practice in genomics. We recently showed that some datasets can be fully re-identified by using entirely free, publicly accessible Internet resources. I will present quantitative analysis about the probability of identifying US individuals by this technique on hundreds of genetic datasets. In addition, I will demonstrate the power of our approach by tracing back the identities of multiple whole genome datasets in public sequencing repositories.

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AUG 21, 2013 12:00 PM PDT

Noninvasive Cancer Genomics

Speaker: Charles Cantor, PhD

Whenever there is cell death, apoptotic cell free DNA fragments appear in the circulation of the host. These fragments, typically 145-160 base pairs in size, represent a minute fraction of total DNA in the host circulation. If care is taken to avoid host cell breakage, the apoptotic DNA fragments can be analyzed to provide information about the genome of the cells that produced them. In pregnancy, analysis of apoptotic DNA fragments has allowed the development of very effective noninvasive aneuploidy testing. Indeed it is possible to reconstruct the entire fetal genomic DNA sequence from these fragments. In cancer it is possible to view copy number, sequence, and epigenetic differences between the tumor and the host by analyzing circulating free DNA. While this work is still at early stages it is reasonable to predict that an array of useful noninvasive cancer diagnostic tests should soon result from such studies. It is furthermore likely that a careful search for informative apoptotic DNA fragments that differ in methylation from DNA in the circulation of a normal host might lead to methods for the early detection of other clinical situations that are characterized by inappropriate cell death.

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AUG 21, 2013 01:00 PM PDT

Bioinformatics and Quantitative Genomics in Cervical Cancer Screening

Speaker: Bruce K Patterson, MD

Cervical cancer screening has evolved significantly since the PAP smear was introduced in 1949. In particular, the association with human papillomavirus (HPV) infection and the mechanism of HPV-related carcinogenesis have been elucidated over the last 20 years. Diagnostics quickly followed focusing on the presence or absence of HPV. Because HPV is ubiquitous and the presence of a high risk type of HPV results in high grade cervical lesions in a small number of instances, the field has realized that infection by HPV is not enough to appropriately triage affected individuals into treatment categories. Detection of HPV DNA has high sensitivity (95%+) for high grade cervical lesions but low specificity (

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AUG 21, 2013 01:00 PM PDT

Codon optimization: new safety concerns for gene therapy and genetic vaccines

Speaker: Vincent P Mauro, PhD

Codon-optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. It is used extensively for expressing recombinant protein drugs, gene therapy, and DNA/RNA vaccines. However, it is becoming increasingly clear that codon-optimization can affect protein conformation and function, increase the immunogenicity of recombinant protein drugs, and reduce efficacy. This presentation will analyze the mechanisms and assumptions underlying codon optimization and identify additional hazards associated with this approach, including unique hazards for gene therapy and DNA/RNA vaccine applications.

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AUG 21, 2013 01:00 PM PDT

In sickness and in health: variables effecting genome sequencing ethical issues

Speaker: Kimberly Strong, PhD

In addition to the exciting promise that genome sequencing holds, concerns are also often described. These concerns relate to: privacy/confidentiality of findings; impact of findings on insurability and discrimination; autonomy and the impact of one's findings on others; questions of clinical utility; the potential for psychological distress; and equity of access. While each of these concerns may constitute a reason for some not to pursue sequencing technology at this time, others remain ready and willing to move forward immediately. Clearly the weighing of risks and benefits are different for different people. Delineating these differences will take time and require empirical exploration. One seemingly obvious bot often neglected differentiation is the starting point for individuals (or family members) - whether they are sick or healthy. Decision making in the context of illness likely (and understandably) influences the weightings given to risks and benefits - perhaps even reframing the balance of promise and concern entirely (a "game changer"). This talk will present the various concerns put forward regarding genome sequencing and discuss the ways in which these are more and/or less relevant depending upon one's relative health situation.

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AUG 21, 2013 02:00 PM PDT

Claritas Genomics: The Future of Pediatric Diagnostics is Now

Speaker: Patrice Milos, PhD

Increasingly genome sequence knowledge is unraveling the complexity of rare Mendelian disorders offering hope for our children's medical care through better disease diagnosis and ultimately patient care. When combined with the emerging new sequencing technologies, allowing large scale genome analysis to move rapidly into clinical laboratories, new opportunities arise for more precise medical care. Claritas Genomics was founded to deliver on the promise of science and technology merging for medical care. Our presentation will discuss the current needs for molecular diagnostics in pediatric populations and provide a better understanding of the role Claritas plays in enabling better patient decisions. Founded as a genetic diagnostic testing company, Claritas combine the power of next-generation DNA sequencing technology with the clinical expertise of the world's best pediatric specialists to assist in informing and improving patient care. Claritas offers a full range to support physician test ordering and support needed as they care for patients, navigating an increasingly complex landscape of genetic diagnostics. Our genomic interpretive services are based on the most up to date and reliable scientific findings and our reports are designed to clearly communicate this complex genetic information. Originally Boston Children's Hospital's CLIA molecular testing laboratory, and launched as an independent CLIA/GLP laboratory in February 2013, we have an existing comprehensive menu of tests, with new next-generation sequencing-based services to be launched in the fall of 2013. Through our partnership with Life Technologies, Claritas is also well positioned to offer cutting edge advances in DNA sequencing, offering products from single gene tests through to whole exomes. Claritas also maintains a close relationship with Boston Children's and its renowned investigators, to uniquely position us to translate novel research-based discoveries into diagnostic clinical practice. Thus we aim to enable health care providers to integrate genomics into the future of their routine medical practice responsibly and Claritas takes pride in our partnership with both our ordering clinicians and the genetic researchers making discoveries that will lead to new tests and clinical knowledge.

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AUG 21, 2013 02:00 PM PDT

Comprehensive Chromosome Screening in the Human Embryo

Speaker: Nathan R Treff, PhD

The human species is particularly prone to chromosome segregation errors during maternal meiosis in the egg and during post zygotic mitosis in the preimplantation embryo. In fact, aneuploidy represents the most common genetic abnormality in humans, and is the primary cause of infertility, affecting 1 in 6 couples. Despite the extremely limited amount of DNA available from a human embryo, development of genetic technologies, such as qPCR and next generation sequencing, now allow accurate and effective analysis of the copy number of all 24 chromosomes in preimplantation stage human embryos produced during in vitro fertilization (IVF). Selection of chromosomally normal embryos improves the efficacy of single embryo transfer, eliminating the primary complication of IVF (multiple gestations), and improves the success of treating infertility. This presentation will detail the development, validation, and future directions of new human embryo comprehensive chromosome screening technologies.

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AUG 21, 2013 02:00 PM PDT

The role of protective genes in the exceptional longevity of humans

Speaker: Nir Barzilai, MD

Aging is the major risk for diseases such as cancer, AD, type 2 Diabetes mellitus and cardiovascular disease. We hypothesize that a progress in preventing these diseases will occur only if we can understand the reason people age at different rates, and develop strategy to delay aging. Certainly the environment plays a major role in our aging, and environmental intervention, such as caloric restriction, can delay aging significantly in many biological models. While we can measure biological changes with aging we cannot assume they are the cause. In fact the challenge is to determine which changes may be the cause/s of aging and which are protective mechanisms against the changes that occurs. One approach to understand aging is to study the oldest old people who are relatively healthy. We established such a unique cohort of individuals with exceptional longevity (~600 Ashkenazi Jews ages 95-112) and their offspring (approximate age 70 years) and age- and sex-matched controls without a family history of unusual longevity. This matched group of offspring of exceptional longevity-proband and their controls are a powerful tool for identifying genetically controlled longevity traits.

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AUG 21, 2013 03:00 PM PDT

Discovery, Development, and Clinical Validation of Gene Expression Scores for Transplant Rejection and Coronary Artery Disease

Speaker: Steven Rosenberg, PhD

Introduction Although the focus of the genomics community has largely been on DNA polymorphisms which affect disease risk, gene expression, especially of blood cells, has the potential to reflect genetic and environmental factors and to inform on both current and future disease status. The immune system dysregulation underlying many human diseases, including transplant rejection, and coronary artery disease (CAD), coupled with development of global blood gene expression profiling and quantitative RT-PCR, has enabled the clinical use of blood-based gene expression tests. Methods Blood samples were obtained from heart transplant or coronary disease patients and paired with results from gold standards of pathologist core-lab read endomyocardial biopsies (EMB) or quantitative coronary angiographic analysis on invasive angiograms, respectively. Discovery, development and validation steps were used to identify genes, develop algorithms, and validate algorithm performance with pre-specified statistical and clinical analysis plans. Development and validation cohorts were obtained in prospective multi-center trials. Finally, the performance and impact of these tests on usual care was assessed in observational or interventional studies. Results For heart transplant rejection largely independent cohorts were used to discover and develop an 11 gene algorithm to discriminate high-grade rejection from quiescence. In a set of independent patient blood samples the ROC curve AUC was 0.72; subsequent comparison of this algorithm with EMB in a prospective interventional trial met the primary endpoint of non-inferiority with a significant reduction in EMB. For CAD diagnosis, after gene discovery by microarrays, independent cohorts from a multi-center angiographic study were used to develop and validate a 23-gene whole blood RT-PCR based algorithm to discriminate obstructive CAD, with a second validation study assessing performance in patients referred for myocardial perfusion imaging. ROC AUC in these two validation studies were 0.70 and 0.79, respectively. Conclusions Blood-based gene expression tests have been developed and are being using clinically.

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AUG 21, 2013 03:00 PM PDT

Evolution of Alu elements in long non-coding RNA and mRNA

Speaker: Daniel Caffrey, PhD

Long non-coding RNAs (lncRNA) are a novel class of RNA molecule that are emerging as important regulators of gene transcription and post-transcriptional events. lncRNAs have been shown to regulate a broad variety of biological processes and are often located within regions of the genome that are associated with various diseases. Repetitive elements are a major component of lncRNA and their molecular functions in lncRNA are poorly understood. Here, I describe the evolution of Alu elements in lncRNA and mRNA. Alu elements are the most abundant transposable element in the human genome (more than 1 million copies) and their composition and evolution within lncRNA and mRNA differ significantly. These striking differences are correlated with their expression and suggest a common molecular function in lncRNA and mRNA.

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AUG 21, 2013 03:00 PM PDT

Investigating tissue specificity of cancer-causing germline mutations

Speaker: Jessica C Mar, PhD

The remarkable diversity we see between different cell types in the human body is governed by the specificity attained through transcriptional and epigenetic regulatory programs. Cancer is a disease that targets specific tissues, and in the case of cancer-causing germline mutations, it is perplexing that primary tumors arise in a restricted subset of tissues only. Understanding why a mutation can be suppressed in one tissue but not others stands to unlock insights into tissue-specific transcriptional regulation and how these programs promote fragility or resistance of cancer-causing mutations. We have been studying cancer-causing germline mutations in the context of cell type-specific gene regulatory networks. Using a comprehensive tissue expression atlas from the FANTOM5 consortium, we have access to CAGE sequencing data that captures promoter usage and gene expression in over 1000 human samples, including primary cells, tissues and cell lines. Levering information from COSMIC, the Cancer Gene Census, and FANTOM5, two classes of genes that have tissues-specific, cancer-causing mutations have been identified - (1) genes that are expressed in the cell type where the cancer occurs, (2) genes that are expressed ubiquitously across many different cell types. For this second class, we have begun comparing regulatory networks associated with these genes in susceptible versus resistant cell types to identify changes in network topology that may change a cell type's oncogenic potential.

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AUG 21, 2013 04:00 PM PDT

Development of Targeted Next Generation Sequencing for Pharmacogenomics

Speaker: Edward Ki Yun Leung, PhD

The goal of personalized medicine is to customize healthcare to the individual patient. Pharmacogenomics, the analysis of how a patient's genetic makeup affects the individual's response to certain drugs, plays a major role in the realization of personalized medicine. Pharmacogenomics studies the influence of genetic variation on the patient's drug response by correlating single-nucleotide polymorphisms (SNPs) with the drug's efficacy and/or toxicity, and therefore with the hope of optimizing drug therapy with respect to the patent's genotype, to ensure maximum efficacy with minimal adverse effects. Currently, most pharmacogenomic studies have been done using DNA chip arrays. A large amount of genetic information is generated in a cost effective way when using DNA chip arrays. However, one limitation of using this technology is that only a subset of mutations are analyzed and different manufacturers may use different SNPs to identify the same haplotype. Recent technological developments with next-generation sequencing (NGS) have enabled pharmacogenomics analysis at costs approaching to the cost of using DNA chip arrays. The advantage of using NGS is that all the SNPs corresponding to a haplotype can be analyzed. Currently, there are only a few targeting-sequencing kits for pharmacogenomics are commercially available. Because these kits may not cover some SNPs of interest, custom sequencing panels are needed to ensure that all interested SNPs are covered. This presentation will go over some of the important features of some commonly used targeted-enrichment technologies for NGS that are desirable for pharmacogenomic studies. This presentation will also highlight some of the challenges of developing and implementing pharmacogenomic NGS in a clinical laboratory for routine patient sample analysis.

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AUG 21, 2013 04:00 PM PDT

Lighting up the dark matter of the genome: Unravelling the roles of noncoding DNA in disease and development

Speaker: Marcel Dinger, MSc (hons), PhD

Approximately 98% of the human genome comprises noncoding DNA, the function of which is largely unknown. Intriguingly, more than 85% of single nucleotide polymorphisms identified to be associated with disease in genome-wide studies (GWAS) occur within noncoding regions, suggesting that examining the role of these regions of the genome will be important for understanding and potentially treating disease. The relatively recent discovery of widespread transcription of potentially functional long noncoding RNAs (lncRNAs) from the mammalian genome led us to investigate whether or not GWAS hits in noncoding regions could be reconciled by the transcription of regulatory RNAs from these loci. LncRNAs typically show highly developmental-stage- and tissue-specific expression, and therefore cannot be easily detected by conventional RNA-Seq, which requires exponentially greater depth to detect increasingly rare transcripts. To overcome this problem, we developed a technique termed RNA-Capture-Seq, which combines custom capture tiling arrays with RNA sequencing to target transcription arising from specific areas of the genome. We have used this approach to target 300 chromosomal regions identified by GWAS. Using RNA from diverse human tissues, we identify thousands of novel transcripts associated with the majority of the targeted regions. To further realise the potential of the method to understand specific diseases, we have designed further capture arrays to target GWAS regions linked to specific diseases. For these experiments, RNA from biologically relevant normal and disease tissues were used to look for novel transcripts. As a result, we have identified numerous new lncRNAs whose expression appears to be specifically associated with disease and arise from disease-associated regions. Although functional investigation of these transcripts is still underway, we propose that the results of these experiments bring an intriguing new perspective into our understanding of how information in the genome is encoded and has considerable potential to identify novel regulators, which may prove valuable as biomarkers and therapeutic targets, involved in disease and development.

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AUG 21, 2013 04:00 PM PDT

The hidden layer of RNA regulation in human development

Speaker: John Mattick, PhD,AO, FAA, FRCPA

High throughput transcriptomic analyses have shown that most of the human genome is dynamically transcribed to produce an extraordinary range of overlapping and interlacing intronic, intergenic and antisense RNAs, many of which are alternatively spliced, to produce a previously hidden universe of long and short regulatory RNAs. These RNAs fulfill various functions in gene expression, with miRNAs and related species being best (although not well) understood. The functions of the long noncoding RNAs (lncRNAs), which range from hundreds to hundreds of thousands of bases in length, are varied and include central roles in the formation of various differentiation-specific subnuclear organelles. However, recent evidence suggests that the major function of lncRNAs is to guide chromatin-modifying complexes to their sites of action, to specify the architectural trajectories of development and differentiation. In addition, it appears that these RNAs are subject to context-dependent editing, particularly in the brain, which appears to be, along with transposon mobility, the molecular basis of physiological and cognitive plasticity. The transcriptome is in fact far more complex than the genome, which is best viewed as a zip file that is unpacked in highly cell-specific patterns during development. Focused RNA sequencing (using oligonucleotide capture to target specific loci, similar to exome sequencing) reveals thousands of previously unknown exons and spliced isoforms of oncogenes and tumor suppressors, as well as a rich landscape of lncRNAs expressed from genomic regions, including GWAS regions associated with complex diseases, that superficially appear to be transcriptionally bare by conventional deep sequencing. Not surprisingly, it is also emerging that variations in the sequence or expression of these RNAs not only underpin phenotypic differences between individuals and species, but also play significant roles in the etiology of complex diseases, including as cancer and neurological diseases.

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AUG 21, 2013 05:00 PM PDT

Fungal Genomics for Energy and Environment

Speaker: Igor Grigoriev, PhD

There are over 1.5 Million fungal species and they play critical role in shaping Earth ecosystems. Better understanding of pathogens and symbionts is critical for a sustainable growth of plants. Fungi are the most efficient degraders of plant biomass to convert it into bioenergy. Many other new metabolic processes and enzymes are encoded in fungal genomes. Fungal genomics may offer answers to critical challenges of future such as food, medicine, energy and the environment. This talk will describe approaches used in large scale genomics- to explore phylogenetic and ecological diversity of fungi. It will also illustrated how genomic data can improve our understanding of plant-fungal interactions and enable practical applications for energy and the environment.

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AUG 21, 2013 05:00 PM PDT

Global penetration of genomic-like techniques into fast clinical diagnostics of infective diseases in emergency: applicability and technological bottle-necks?

Speaker: Ivan Brukner, PhD

Dr Ivan Brukner entered into genomic era back in 1989 (ex-Yugoslavia), trying to describe and solve repeating sequence "branching motif problem" in building whole genome sequence. Next 5-10 years, his research was targeting sequence-dependent DNA structural problems, where contradictory puzzle about origin of DNA curvature and bending (crystallographic versus soft biochemistry data) was resolved (Italy, Germany and Canada). In 2000-2007, focus was directed toward design of nucleic-acid-based "ideal" point of care diagnostic device. Robust, multiplex, hybridization-based diagnostic device (which operates at standard "room" temperatures - in spite of ~90% sequence cross-similarity) was constructed and functionally tested. The universal protocol for selection of "robust" hybridization probes was result of this adventure. After joining Jewish General Hospital in Montreal (~2009), his work was becoming more clinically applicable, focusing on high volume molecular assays with strong financial and/or diagnostic impact (MRSA, C.difficile, VRE). He realized the strong need for applicability of new molecular techniques in emergency, including NGS, and definition of technological bottlenecks is subject of his talk in this secession.

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AUG 22, 2013 07:00 AM PDT

Metabolic reprogramming: links to the epigenome

Speaker: Kathryn E Wellen, PhD

Cancer cells are characterized by major alterations in both cellular metabolism and epigenetic profiles. Current understanding of links between metabolism and chromatin in the context of cancer is currently very limited. We have previously demonstrated that acetylation of histones is sensitive to glucose availability through the enzyme ATP-citrate lyase (ACL), which produces acetyl-CoA from citrate. While this is likely to impact gene expression and other chromatin-dependent processes, the molecular mechanisms and functional significance of metabolic regulation of lysine acetylation are poorly understood. In this presentation, I will focus on current efforts to elucidate how metabolic signals are conveyed to chromatin. I will also discuss recent findings demonstrating a novel link between ACL and another chromatin-modifying enzyme, DNA methyltransferase 1, during adipocyte differentiation.

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AUG 22, 2013 07:00 AM PDT

Soluble 14-3-3? - A Personalised Rheumatoid Arthritis Patient Management Strategy

Speaker: Anthony Marotta, PhD

Rheumatoid Arthritis (RA) is a heterogenous disease that affects 1.5% of the population. Similar to cancer, early detection coupled with an effective treatment strategy can significantly improve patient outcomes. In the advent of new classes of RA therapies, there is an impetus to identify new serological markers that mark risk of RA development, prognosis and therapy response. 14-3-3 eta (?) is a new RA marker that is available for clinical use in the US through Quest Diagnostics. 14-3-3? is one of 7 members of the 14-3-3 family and is specifically present in the serum of patients with RA and erosive psoriatic arthritis (PsA). In the healthy state, these proteins reside within the intracellular space governing various biological processes including proliferation, differentiation and metabolism. Increased expression of different 14-3-3 isoforms correspond with worse prognosis in certain cancers and neurological disorders. In RA, the 14-3-3? protein is specifically externalized and can be measured in serum, making it a useful clinical serum marker. When 14-3-3? exists in the extracellular environment, it behaves as a soluble ligand inducing factors that drive inflammation and joint damage also making it a novel therapeutic target. This presentation will describe the discovery of 14-3-3? in arthritis, its development pathway and the biomarker's clinical utility. We will discuss how the 14-3-3? biomarker pipeline has evolved from the protein R&D programs into a 14-3-3? biomarker suite that serves as a direct companion to a first-in-class RA personalized medicine drug target.

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AUG 22, 2013 07:00 AM PDT

Warfarin Sensitivity Testing

Speaker: Thomas P Moyer, PhD

Anticoagulation therapy is frequently employed to prevent stroke in patients with atrial fibrillation, prophylaxis of venous thromboembolism and pulmonary embolism in patients with prosthetic heart valves and myocardial infarction, and prevention of pulmonary embolism or deep vein thrombosis after orthopedic surgery or with a history of venous or arterial thromboembolism. Warfarin is an effective anticoagulant that can be prescribed for prolonged periods of time. However, warfarin causes adverse events; if under-dosed, clots may form causing stroke, and if overdosed, life-threatening bleeding may occur. Rivaroxaban and dabigatrin have recently come on the market as warfarin alternatives. While these drugs are reported to produce fewer adverse events, clinical experience suggests otherwise; adverse events do occur. More importantly, there are no reversal agents for these new drugs; managing an anticoagulant induced bleed by one of these agents is difficult. Pharmacogenomic (PG) testing has been applied to warfarin to reveal genetic variants that predict warfarin adverse events. The liver enzyme Cytochrome P450 2C9 metabolizes warfarin. Three variants have been extensively studied; these variants decrease warfarin metabolism predisposing patients to warfarin overdose. The enzyme Vitamin K Epoxide Reductase, known as VKORC1, converts Vitamin K to the reduced form required to activate clotting factors II, VII, IX, and X. Genetic variants in VKORC1 decrease enzyme activity causing warfarin to induce a more profound decrease in activated clotting factors than normal. Patients with this variant are more likely to experience warfarin-induced bleeding. Application of PG testing to large patient populations suggests that modified warfarin dosing based on results of PG reduce warfarin adverse events by more than 35%; this makes warfarin essentially equivalent to rivaroxaban in terms of efficacy. Summing the benefits of 50 plus years clinical experience with warfarin, availability of a reversal agent for warfarin-induced bleeding, and availability of PG testing to guide dosing, warfarin may be the safest anticoagulant on the market today.

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AUG 22, 2013 08:00 AM PDT

Aliens, Computers & Engineering Biology - An Introduction to Synthetic Biology

Speaker: Drew Endy, PhD

Synthesis and assembly of DNA powerfully enables reverse genetics-based approaches to scientific discovery. I'll present recent and unpublished work on genome refactoring and redesign, focusing on identification of cryptic genetic elements and genome decompression. Next, I'll summarize work published over the past year in which we reported the first non-volatile and rewritable digital genetic data storage systems, amplifying genetic logic gates, and programmed cell-cell communication via arbitrary DNA messages. These experiences will be used to frame ten years of research in synthetic biology, by which the foundational engineering ideas of abstraction and standardization have finally been shown as not impossible to make true, and that when made true enable our designer DNA systems to work reliably the first time.

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AUG 22, 2013 09:00 AM PDT

Management and Analysis of Pre-implantation Genetic Diagnosis Data

Speaker: Deanne Taylor, MS, PhD

During IVF procedures pre-implantation genetic diagnosis (PGD) allows for genetic profiling of embryos prior to replacement. Most PGD procedures during IVF are performed to select chromosomally normal embryos as comprehensive chromosome screening (CCS), and in a smaller number of cases PGD is used for embryo selection against known genetic disease variants carried by the parents. Genomic technologies utilizing PCR, microarray, and second-generation sequencing methods are currently being used for PGD data analysis in the laboratory. With decreasing costs in second-generation sequencing technologies coupled with increased demand for PGD, adoption of "PGD-seq" methods for CCS and genetic selection will face significant future challenges in data management, analysis and information delivery to clinicians. One of our goals is to provide secure, integrated environments for clinicians to use genetic information to inform treatment strategies. I discuss challenges and strategies for storing and integrating biomedical data with other private and public data repositories. I discuss process and warehouse design, analysis methods and implementation strategies for PGD and genetics data. I discuss how we deliver and visualize PGD data for clinicians and to researchers in clinical and basic science.

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AUG 22, 2013 09:00 AM PDT

Next-Gen Sequencing: Driving the Transition from Genetics to Genomics

Speaker: Shawn Baker, PhD

The rapid advancements in next generation sequencing have served the research market very well, delivering more and more sequence for less and less money. While these advancements are still being made, the market is now looking toward serving a new customer - the clinician. For both technology platforms and informatics solutions, the emphasis is now on speed, quality and ease of use. An understanding of this market and where it is headed will help in predicting the broad implications for the future of medicine.

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AUG 22, 2013 09:00 AM PDT

Return of Genome Sequencing Results to Physicians and Patients

Speaker: Cinnamon S Bloss, PhD

There has been considerable debate in the scientific and clinical communities regarding the return of results from genome sequencing to physicians and patients. Questions surrounding which health care professional(s) should deliver this information, as well as what types of results should be returned loom large. The aim of the Scripps Idiopathic Diseases of huMan (IDIOM) study is to use genome sequencing to inform diagnosis and treatment of idiopathic diseases. As part of this study, we assess patient and provider preferences surrounding the types of results returned from sequencing, as well as perceptions of the return-of-results communication itself. This is done via semi-structured interviews and standardized questionnaires. Data collected to date suggest that the majority of probands and their parents would prefer, if given the choice, to receive sequencing results for the presenting condition, as well as secondary findings in multiple disease categories (e.g., actionable and non-actionable, childhood and adult-onset). Further, data from the completed return-of-results sessions suggest notable variation in patient satisfaction with communication of results by the referring physician. This includes, in some cases, a marked discrepancy between the extent to which the physician felt results were communicated effectively versus the extent to which the patient perceived the communication to be effective. These case-by-case findings will be discussed in detail. Through the Scripps IDIOM study we have begun collection of empirical data on patient preferences and perceptions regarding return of results from genome sequencing for diagnosis and treatment of idiopathic disease. It is our hope that these data will help inform the development of an effective, sustainable, and cost-effective model of return of individual results from genome sequencing in clinical settings.There has been considerable debate in the scientific and clinical communities regarding the return of results from genome sequencing to physicians and patients. Questions surrounding which health care professional(s) should deliver this information, as well as what types of results should be returned loom large. The aim of the Scripps Idiopathic Diseases of huMan (IDIOM) study is to use genome sequencing to inform diagnosis and treatment of idiopathic diseases. As part of this study, we assess patient and provider preferences surrounding the types of results returned from sequencing, as well as perceptions of the return-of-results communication itself. This is done via semi-structured interviews and standardized questionnaires. Data collected to date suggest that the majority of probands and their parents would prefer, if given the choice, to receive sequencing results for the presenting condition, as well as secondary findings in multiple disease categories (e.g., actionable and non-actionable, childhood and adult-onset). Further, data from the completed return-of-results sessions suggest notable variation in patient satisfaction with communication of results by the referring physician. This includes, in some cases, a marked discrepancy between the extent to which the physician felt results were communicated effectively versus the extent to which the patient perceived the communication to be effective. These case-by-case findings will be discussed in detail. Through the Scripps IDIOM study we have begun collection of empirical data on patient preferences and perceptions regarding return of results from genome sequencing for diagnosis and treatment of idiopathic disease. It is our hope that these data will help inform the development of an effective, sustainable, and cost-effective model of return of individual results from genome sequencing in clinical settings.

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AUG 22, 2013 10:00 AM PDT

Clinical Interpretation of Sequence Variants

Speaker: Elaine Lyon, PhD

The advent of massively parallel sequencing by next generation sequencing platforms now allow genomic approaches for individualizing healthcare. Genomic sequencing data reveals variants in genes related to drug metabolism that may affect efficacy or response. This presentation will describe the potential of NGS data for companion diagnostics or therapeutics and its implementation into clinical laboratories. Evaluating pharmacogenetic targets through exome analysis as well as through targeted gene panels will be discussed.

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AUG 22, 2013 10:00 AM PDT

FarGen - a holistic genomic health approach

Speaker: Bogi Eliasen, MSc

The FarGen project aims to sequence the whole genome of the entire Faroese population. Together with existing genetic records, such a comprehensive sequencing project can significantly improve treatment and prevention services in the Faroese public health system. The project has also great potential in an international research context as it can contribute significantly to our general understanding of human genetics. An understanding of genetics has proved crucial in health systems of the future, and genetic studies are already being used in Faroese health system. And with the introduction of the Human Genetics Act and the Genetic Biobank in 2006, the stage was set for a thriving genetic research environment in the Faroe Islands. The digitalisation of the Faroese genome, combined with the extensive health records in the Faroese health system, will significantly boost our general understanding of health issues, resulting in improved treatment and prevention services in the Faroe Islands. Thanks to our coherent health system, our special legislation (the Human Genetics Act), our digital public health register, and not least our digitalised genealogy records, the FarGen project has attracted a great deal of interest from international researchers. With these unique features, the Faroe Islands may well the ideal place for incorporating genetic research into the public health system. Both education and the ELSI play a significant role in a nationwide project like the FarGen and parallel to the sequencing a educational system for both health staff, school and the general public is been developed.

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AUG 22, 2013 10:00 AM PDT

Using Prostate Cancer Exome Data to Identify Candidate Genes

Speaker: Matthew Keyser, MS

In this presentation, exome data from individuals with prostate cancer will be aligned against an annotated reference human genome and SNPs will be identified using DNASTARs SeqMan NGen software. SNPs and associated genes from disease samples will be compared against numerous control samples and a list of genes known to be implicated in prostate cancer or other cancers to identify additional candidate SNPs and genes in sample data. All work will be done using DNASTARs Lasergene Genomics Suite software, which is available on desktop computers or on the Amazon Cloud. The integration of these capabilities within one software package facilitates fast, comprehensive analysis, helping researchers move quickly from raw next-generation sequence data to informative results.

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AUG 22, 2013 11:00 AM PDT

Design of protein structures, functions and assemblies

Speaker: David Baker, PhD

I will describe recent advances in computational protein design which allow the generation of new protein structures and functions. I will describe the use of these methods to design ultra-stable idealized proteins, flu neutralizing proteins, high affinity ligand binding proteins, and self assembling protein nanomaterials. I will discuss possible applications to therapeutics, vaccines and diagnostics. I will also describe the contributions of the general public to these efforts through the distributed computing project Rosetta@home and the online protein folding and design game FoldIt.

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AUG 22, 2013 12:00 PM PDT

Exome Sequencing as a Diagnostic Tool

Speaker: Pinar Bayrak-Toydemir, MD, PhD

It is widely accepted that approximately 85% of known disease-causing DNA variants affect the exons and splice junctions, which is about 1% of the whole genome. As a result, Clinical Exome Sequencing is a powerful and highly efficient diagnostic tool to identify disease-causing DNA variants in individuals. In this talk, I will discuss the methodology, validation, reporting, and bioinformatics aspects of clinical exome sequencing. In addition, I will talk about the regulations regarding reporting of incidental findings and the American College of Medical Genetics guidelines. I will include discussion of advantages and disadvantages of the methodology based on examples of positive and negative clinical exome sequencing results.

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AUG 22, 2013 12:00 PM PDT

Use of Whole Genome Sequencing in Clinical Practice

Speaker: Howard J Jacob, PhD

Howard J. Jacob, Ph.D., Founding Director of the Personalized Medicine Program and Human and Molecular Genetics Center and Professor in Physiology and Pediatrics at the Medical College of Wisconsin and Children's Hospital of Wisconsin. In 2010 Dr. Jacob led a team of researchers at the Medical College who for the first time ever were able to use the human genome to diagnose and treat a young boy, Nicholas Volker whose life threatening disease had baffled his doctors. Nik is now leading a fully and healthy life. Dr. Jacob completed his Ph.D. at the University of Iowa followed by fellowships at MIT, Harvard and Stanford. He has published over 230 papers. He is an entrepreneur and serves on several scientific advisory boards.

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AUG 22, 2013 01:00 PM PDT

Dominant regulation of gene expression by microRNAs

Speaker: Noam Shomron, PhD

MicroRNAs are short non-coding cellular regulators of gene expression. Each microRNA controls the expression of a large set of genes, and microRNAs collectively, may regulate more than half of human genes. In the laboratory, our team focuses on understanding the function of microRNAs in health and during disease. We map their expression in developing cancer cells and in various brain disorders. We predict direct gene targets of these microRNAs sets and then pinpoint the cellular pathways affected. I will present our recent findings in the field and discuss its potential implications for prognosis and diagnosis. Overall our team pursues research that aims to deepen our understanding on the development of diseases in order to generate a significant impact through translating ideas into clinical reality.

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AUG 22, 2013 01:00 PM PDT

Embracing the Complexity of Cancer: Seeing the Forest and the Trees

Speaker: Kenneth Buetow, PhD, FACMI

Personalized medicine is transforming biomedical research and healthcare service delivery. Disease definition, diagnosis, treatment, and prevention are being fundamentally altered by the capacity to routinely perform comprehensive molecular characterization. Nowhere is this change happening faster than in the field of cancer. Increasingly sophisticated technology provides the capacity to describe, in multiple molecular dimensions, the tumor and the individual in which it has developed. These technologies identify the millions of variants present in normal individuals and thousands of alterations that occur during the course of the disease process. This systems-wide molecular analysis of constitutional and somatic tissues has identified a complex cacophony of inherited and acquired variation. Coherence emerges from these data when evaluated using biologic networks as analytic frameworks. These networks account for the individual heterogeneity in underlying etiology as well as the diversity of events necessary to generate a complex phenotype such as cancer. Emerging collections of analytic approaches permit analysis using genome-wide data sets and established biologic networks as models. The generation of this unprecedented amount of data presents us with the challenge contextualizing that data and converting into actionable information. The integration and interpretation of this complex multidimensional information into the evidence necessary to support clinical care exceeds the raw human cognitive capacity. Information systems have the capacity to provide the needed "tool" to tackle this challenge - to generate the necessary evidence to support the delivery of personalized medicine. Arizona State University's (ASU) Complex Adaptive Systems team is building such an Evidence Engine in its Next Generation Cyber Capability (NGCC). The ASU NGCC - composed of networks, hardware, software, and people transforms "Big Data" to information and creates the evidence necessary to enable personalized medicine.

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AUG 22, 2013 02:00 PM PDT

The Road to Genomic Medicine is Paved with Data and Information

Speaker: John Quackenbush, PhD

Since the introduction of second-generation DNS sequencing technologies in 2007, the cost of genome sequencing has been consistently by 33% per quarter, with the $1000 genome arriving in 2012 and the $100 genome not far off. As DNA sequencing increasingly becomes a commodity, biomedical research is rapidly evolving from a purely laboratory science to an information science in which the winners in the race to cure disease are likely to be those best able to collect, manage, analyze, and interpret data. Here I will provide an overview of the approach we have been developing to deal with the challenge of personal genomic data, including integrative approaches to data analysis and the creation of data portals focused on addressing the most common use cases presented by different user constituencies. By effectively collecting genomic and clinical data and linking information available in the public domain, we have made significant advances in uncovering the cellular networks and pathways that underlie human disease and building predictive models of those networks that may help to direct therapies.

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AUG 22, 2013 02:00 PM PDT

Translation and Clinical Application of Innovative Genomic Analysis: Challenges Remain

Speaker: Paul Billings, MD, PhD

The role of the human genome in normal and patho-biology is crucial. Applied in cancer care and in a variety of unknown disorder settings, it can provide key insights and crucial diagnostic/prognostic/predictive/other information. Its methods can also help improve clinical practices already provided. But many challenges remain that could delay its beneficial application, increase errors, or add unnecessary costs. In this talk, I will review the field of clinical genomic analysis generally and then focus on important challenges in its translation and clinical applications.

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AUG 22, 2013 03:00 PM PDT

Evaluation challenges and regulatory considerations for next-generation sequencing and other high throughput genomic technology based clinical applications

Speaker: Živana Težak, PhD

The use of ultrahigh throughput diagnostic tests that determine genetic sequence variation to guide patient care is rapidly expanding, fueled by the enormous growth in sequencing platform development. With the emergence of novel technologies, the FDA is faced with new regulatory challenges while continuing to apply scientific evidence-based oversight. While there are no broadly accepted standards or methods to analytically validate ultrahigh throughput sequencing tests yet, there are a number of efforts underway, including establishing reference materials to aid in assessing analytical performance. The additional challenge in informed clinical application of sequence information is inadequate knowledge about correlations between genomic variations and their clinical significance. The FDA is proactively working to encourage cross-collaboration in this area. Ultimately, the FDA has to balance public safety concerns with fostering innovation and enabling the translation of emerging technologies that can improve medical care and benefit public health.

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AUG 22, 2013 03:00 PM PDT

Next-generation Cancer Care in the Age of Genomics, Precision Medicine, High Throughput Biology

Speaker: C Jimmy Lin, MD, PhD, MHS

Developments in DNA sequencing technology have provided a unique opportunity for diagnosis and discovery of genetic alterations for rare diseases. Partnering with 20 academic centers in the US and globally, we have coordinated and facilitated NGS projects for rare disease. We will summarize what we learned from all these sites for the entire process from consent, sample collection, library prep, sequencing, bioinformatics, interpretation, counseling, and clinical reimbursement.

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AUG 22, 2013 04:00 PM PDT

Complexity of Mammalian Transcription

Speaker: Piero Carninci, PhD

The next generation sequencing technologies are profoundly influencing our way to study biology. We have previously developed cap-analysis gene expression (CAGE) to simultaneously mRNA/noncoding RNA starting sites and simultaneously detect their expression. Altogether, CAGE achieves comprehensive coverage of transcription starting site and allows to assign newly discovered promoters/5' ends to the rest of the RNA sequence (CAGEscan technology). With these technologies, we can infer the transcriptional networks that regulate gene expression. This technology is being applied to a broad range of samples to elucidate the promotome and the regulatory networks of mouse and human primary cells and tissues in the FANTOM5 project. DeepCAGE allows also detecting dynamic expression of repeat elements, which show peculiar expression patterns and provide alternative promoters and functional genome elements. We have also used deepCAGE on subcellular fractions as a part of the ENCODE project. We have detected clear patterns of expression of retrotransposon elements (RE) in a panel of human and mouse tissues, which are likely to have a regulatory role. Now, we have clearly identified specific patterns of non-coding RNAs and other RE-derived RNA in different cell compartments, with a particular interesting role of LINE elements, which seem to be preferentially bound to the chromatin. Other retrotransposon elements, like LTRs, are prevalently expressed in ES and iPS cells, where they may have a role to keep the stem cells undifferentiated. Altogether, these data are pointing at a potential function of the retrotransposon elements and other ncRNAs to regulate the epigenome.

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AUG 22, 2013 05:00 PM PDT

Clinical Utility Potential of Epigenetic Aberrations in Human Solid Tumors

Speaker: Dave S Hoon, PhD

As Chief of Scientific Intelligence at the John Wayne Cancer Institute, Dr. Hoon interacts with external academic, industry, and government agencies to develop innovative translational research opportunities. He has coauthored more than 250 peer-reviewed articles and reviews, primarily related to translational molecular oncology of human solid tumors. He has over 25 patents on his studies. As founding Director of the Department of Molecular Oncology, Dr. Hoon continues to pioneer investigations of RNA/genomic/epigenomic biomarkers for diagnostic, prognostic and predictive assessment of residual tumor cells. He also spearheads investigations of circulating DNA/miRNA biomarkers for staging cancer in patients enrolled in phase II/III clinical trials. The Department's focus on biomarker expression in both tissue and body-fluid specimens gives it a uniquely broad scope. Dr. Hoon's team has developed diagnostic tissue biomarkers for molecular staging of sentinel lymph nodes and classification of human solid tumors such as melanoma, breast cancer and gastrointestinal cancer. Dr. Hoon also has pioneered development of blood-based nucleic-acid and tumor-cell biomarkers as prognostic tools. In the last decade he and his team have designed and conducted biomarker companion studies as part of multicenter international clinical trials. On the therapeutic front, Dr. Hoon is examining functional genomic and epigenomic changes as potential targets for development of novel approaches to treat or prevent malignancy. Dr. Hoon and the Department are funded by the National Institutes of Health/National Cancer Institute, the California Breast Cancer Research Program, Susan G. Komen for the Cure, Adelson Melanoma Research Foundation, the United States Department of Defense, and the pharma-biotech industry. Dr. Hoon has served on several review study sections as a permanent member for the National Cancer Institute, and was a founding member of NCI's Cancer Biomarker Study Section. The Department of Molecular Oncology consists of over 20 MD/PhD scientists and research technicians focused on translation molecular oncology. Some of the major ongoing collaborations include: Leiden University Medical Center, Netherlands; Genome Institute Singapore, Biopolis; Broad Institute of MIT and Harvard; Keio University; MD Anderson, and Melanoma Institute Australia. Dr. Hoon has trained more than 60 postdoctoral oncology fellows, who now hold faculty appointments in numerous academic institutions.

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AUG 22, 2013 05:00 PM PDT

Genomic Profiles of Asian Endemic Cancers

Speaker: Patrick Tan, MD, PhD

Malignancies caused by so-called Type I chemical and biological carcinogens provide important opportunities studying early events in cancer development, providing essential information for developing future cancer prevention strategies. In Asia, several highly lethal cancers are known to be caused by pathogens, such as stomach cancers (H. pylori), bile duct cancers (liver flukes), and certain lymphoma subtypes (Epstein-Barr Virus). For many of these conditions, treatment options are still highly limited. In this talk, I will describe how genomic analysis of infection-related Asian cancers can provide insights into cellular processes disrupted by these pathogens, and how such data can be used to identify new therapeutic targets.

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Speakers

Dave S Hoon, PhD

Chief of Scientific Intelligence, Director of Molecular Oncology, John Wayne Cancer Institute
Elaine Lyon, PhD
Associate Professor (Clinical) of Pathology, Division Medical Director, Genetics, Co-Program Director, Clinical Genetics Fellowship Program, Program Director, Molecular Genetics Fellowship Pr

Biography
Dr. Lyon is the medical director of the Genetics Division, co-medical director of Pharmacogenomics, and co-director of the Molecular Genetics Fellowship Program at ARUP, and an associate professor of pathology at the University of Utah School of Medicine. She received her PhD in medical genetics from the University of Alabama at Birmingham and continued with fellowship training in clinical molecular genetics at the University of Utah. Dr. Lyon combines clinical laboratory responsibilities with research and development in human genetics, employing methods for mutation detection by targeted mutation analysis, gene sequencing, gene scanning, exonic-level deletion, and duplications and molecular haplotyping. Dr. Lyon has focused her interest in studies to determine the significance of rare variants and is involved with evaluating and establishing locus-specific databases that combine genetic variants with clinical symptoms.
Deanne Taylor, MS, PhD
Director Bioinformatics, Children's Hospital of Philadelphia, University of Pennsylvania

Biography
Deanne Taylor joined DBHI in 2014 as the Bioinformatics Director. Deanne oversees the design, development, and implementation of high performance innovative bioinformatics workflows and provide technical leadership and supervision of a multidisciplinary bioinformatics team at CHOP. Previously, she was Director of Bioinformatics with Reproductive Medicine Associates and Assistant Professor with the Department of Obstetrics, Gynecology and Reproductive Medicine at Rutgers Robert Wood Johnson Medical School. Prior to that she worked for Harvard School of Public Health as a Research Scientist and served several years as the Program Director of the Graduate Program in Bioinformatics at Brandeis University. She also has experience working in the pharmaceutical industry. Deanne obtained her PhD in Biophysics from the University of Michigan, Ann Arbor, and completed a postdoctoral fellowship at Pfizer. Her background is in biophysics, bioinformatics, computational biology and structural biology with emphasis on human genetics and translational medicine. Deanne's main areas of research are in the development of mathematical and computational methods to better understand biological variation and the genetic contribution to disease, coupling clinical information with high-dimensional biomedical data from next-gen sequencing, microarray, PCR, and proteomics experiments.
Cinnamon S Bloss, PhD
Director of Social Sciences & Bioethics, Assistant Professor, Scripps Translational Science Institute, Scripps Health & The Scripps Research Institute

Biography
Dr. Bloss is an Assistant Professor, as well as Director of Social Sciences and Bioethics at the Scripps Translational Science Institute. Her research is funded by the National Institutes of Health and is focused on investigating individuals' behavioral and psychological responses to disclosure of personal genomic information. She is the lead researcher on STSI's Scripps Genomic Health Initiative, and her work on this project was recently published in the New England Journal of Medicine and has been highlighted at a number of national and international scientific meetings. She has also presented invited testimony on consumer genomics before the Food and Drug Administration Advisory Panel. Dr. Bloss' other research interests include developing ways of combining genomics with traditional disease risk factors to make predictions about disease development, progression and response to treatment, as well as designing effective health interventions that leverage genomic information. She also conducts genetic association studies and has several collaborations to investigate the genetic underpinnings of neurological, behavioral, and other health-related phenotypes. Dr. Bloss received her B.A. in Psychology from Smith College, her Ph.D. in Clinical Psychology from the University of California, San Diego, and completed a predoctoral internship in clinical neuropsychology at the University of Florida. Dr. Bloss completed a post-doctoral fellowship in statistical genetics and genomic medicine at The Scripps Research Institute.
Shawn Baker, PhD
CEO, CSO and Co-Founder, AllSeq, Inc.

Biography
Dr. Shawn C. Baker is the Chief Science Officer and co-founder of AllSeq. Having received his Ph.D. at the University of California - Davis, he started his career as a Research Scientist at Illumina when it was a 15-person startup. After spending several years at the bench developing gene expression array products, he transitioned to Product Marketing where he led a team in charge of Illuminas Expression and Regulation sequencing portfolio. In 2013 Dr. Baker co-founded AllSeq, establishing the only true sequencing marketplace, matching researchers with service providers based on their needs. <br />
Drew Endy, PhD
Assistant Professor of Bioengineering at Stanford, and President of The BioBricks Foundation

Biography
Drew Endy developed the world's first "fabless" genetic engineering teaching lab in the new Bioengineering program at Stanford and previously helped start the Biological Engineering major at MIT. His Stanford research team develops genetically encoded computers and redesigns genomes. He co-founded the BioBricks Foundation as a public-benefit charity supporting free-to-use standards and technology that enable the engineering of biology. He co-organized the International Genetically Engineered Machines (iGEM.org) competition, the BIOFAB International Open Facility Advancing Biotechnology (BIOFAB.org), and Gen9, Inc. (Gen9bio.com). He serves on the US Committee on Science Technology and Law and is a new voting member of the US National Science Advisory Board for Biosecurity. He chaired the 2003 Synthetic Biology study as a member of DARPA ISAT, served as an ad hoc member of the US NIH Recombinant DNA Advisor Committee, and co-authored the 2007 "Synthetic Genomics: Options for Governance" report with colleagues from the Center for Strategic & International Studies and the J. Craig Venter Institute. Esquire named Endy one of the 75 most influential people of the 21st century. He lives in Menlo Park CA with his wife and Stanford Bioengineering colleague Prof. Christina Smolke.
Anthony Marotta, PhD
Chief Scientific Officer, AugureX Life Sciences Corp

Biography
Anthony serves as the Chief Scientific Officer at Augurex Life Sciences Corp, a company that he co-founded with CEO, Mrs. Norma Biln. Anthony's creativity and business acumen have set him apart from most scientific leaders. Anthony has worked in the life sciences space for 20 years and has consistently created progressive opportunities that have delivered great returns for companies that he has been involved with. He received his PhD from the Faculty of Medicine at the University of British Columbia in Vancouver, Canada.
Kathryn E Wellen, PhD
Assistant Professor, Assistant Investigator, Abramson Family Cancer Research Institute, University of Pennsylvania Medicine

Biography
Dr. Kathryn Wellen received a PhD from Harvard University in 2006 and performed postdoctoral work at the University of Pennsylvania from 2006-2011. In 2011 she joined the Department of Cancer Biology at the University of Pennsylvania as an Assistant Professor. She is a 2012 Pew Scholar in the Biomedical Sciences and is a recipient of a 2012 Forbeck Scholar Award. Her laboratory's research focuses on elucidating links between cellular metabolism and signaling, with a current emphasis on metabolic regulation of the epigenome.
Thomas P Moyer, PhD
Professor of Laboratory Medicine, Mayo Clinic

Biography
Thomas P Moyer received a BA in Chemistry from the University of Minnesota in 1970. Following receipt of his undergraduate degree he spent two years in the United State Army Infantry. Upon completing his military service, Moyer entered graduate school at North Dakota State University where he earned the PhD degree in Biochemistry in 1976. He trained at Mayo Clinic as a Fellow in Clinical Chemistry, and joined the medical staff of Mayo Clinic in Rochester, Minnesota in 1979 as a Consultant in the Department of Laboratory Medicine & Pathology. While at Mayo Clinic, Moyer created the Drug Laboratory and lead in the formation of the Nucleotide Polymorphism Laboratory. He was Division Chair of Clinical Biochemistry & Immunology, and served as Vice Chair of the Department of Laboratory Medicine & Pathology and as Senior Vice President of Mayo Medical Laboratories. Dr. Moyer was elected by the medical staff to serve as an Officer of Mayo Clinic in 2000. He has published 108 peer reviewed papers, 123 abstracts, 30 book chapters, and two books. Dr Moyer was also active in the American Association for Clinical Chemistry (AACC) serving in numerous leadership roles, including as President in 2004. He also represented AACC to the International Federation of Clinical Chemistry, serving as a member of the Scientific Division, and a member of the Congress and Conference Division.
Ivan Brukner, PhD

Head of Molecular Microbiology Unit- Molecular Biology, Jewish General Hospital - McGill University
Igor Grigoriev, PhD
Head, Fungal Genomics Program, US Department of Energy Joint Genome Institute

Biography
Dr. Grigoriev joined the DOE Joint Genome Institute in 2003 to participate in human genome annotation and lead annotation of over 200 diverse eukaryotic genomes from protists to plants (http://genome.jgi.doe.gov). In 2009 at JGI he started the Fungal Genomics program (http://www.jgi.doe.gov/fungi) to scale up sequencing and analysis of diverse fungi for related to DOE science and applications, which led to large projects like 1000 Fungal Genomes. Dr. Grigoriev organized over 30 genomics workshops and engaged over 2000 researches around the world in genome projects, which resulted in over 50 high-profile publications.
Bogi Eliasen, MSc
Program director for FarGen, Faroe Islands Ministry of Health

Biography
Bogi Eliasen is a knowledge-broker bringing the expertise of all kinds of disciplines together. He is an expert on international politics and law and manages the first nationwide genome sequencing project in the world, FarGen.
Matthew Keyser, MS
Senior Manager, NGS Applications, DNASTAR

Biography
Matthew Keyser is Senior Manager, NGS Applications for DNASTAR, where he has helped scientists address their sequence assembly and analysis challenges for the past seven years. Matts sole focus at DNASTAR is supporting customers in next-gen sequencing applications using DNASTARs broad software toolset. Matt helps customers with their templated and de novo assembly projects, transcriptomes, exomes, metagenomic assemblies, RNA-Seq, ChIP-Seq and numerous other unique experiments. Matt has helped hundreds of scientists optimize their workflows using DNASTARs next-gen software solutions. He has also spoken at numerous conferences and workshops regarding the capabilities of DNASTARs next-gen software tools.
David Baker, PhD
Investigator, Howard Hughes Medical Institute, Professor of Biochemistry, Adjunct Professor of Genome Sciences, Physics, Computer Science, Chemical Engineering, and Bioengineering, University

Biography
The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended to a distributed computing project called Rosetta@Home and Foldit. The project aims to produce structural models for protein complexes as well as individual polypeptide chains. The Baker group participates regularly and is recognized for expertise in the CASP structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol. Members of the Baker group are also active in the field of protein design; they are recognized as the first group to have designed a protein, known as Top7, with an entirely novel fold. Baker did his graduate work in biochemistry at the University of California, Berkeley in the laboratory of Randy Schekman, where he worked predominantly on protein transport and trafficking in yeast. He did his postdoctoral work with David Agard of University of California, San Francisco. Although well known for development of methods for computational prediction of protein structure and function, Baker is focused on the use of computational methods to drive experimental assessment of biology and therefore the Baker laboratory maintains an active experimental biochemistry group. For his work on protein folding, Baker received the 2008 Sackler International Prize in Biophysics. Baker was elected a Fellow of the American Academy of Arts and Sciences in 2009.
Patrick Tan, MD, PhD
Professor, Cancer & Stem Cell Biology Pgm, Duke-NUS Graduate Medical School Singapore, Sr. Group Leader, Genome Institute of Singapore, Program Leader, Genomic Oncology, Cancer Science In

Biography
Dr. Patrick Tan holds a joint appointment as a Professor at the Duke-NUS Graduate Medical School and Senior Group Leader at the Genome Institute of Singapore. He is also Senior Principal Investigator at the Cancer Science Institute of Singapore, National University of Singapore and Research Associate Professor in the Institute of Genome Sciences and Policy at Duke University, USA. His research focuses on the application of genomics to cancer and infectious disease. He received his B.A. (summa cum laude) from Harvard University and MD PhD degree from Stanford University, where he received the Charles Yanofsky prize for Most Outstanding Graduate Thesis in Physics, Biology or Chemistry. Other honors include the President's Scholarship, Loke Cheng Kim foundation scholarship, Young Scientist Award (A-STAR), Singapore Youth Award (twice), Singhealth Investigator Excellence Award, Han-Mo Koo Memorial Lectureship (Van Andel Research Institute, USA) and Swee Liew Wadsworth Lectureship (NUS). Recently, he received the Chen New Investigator Award from the Human Genome Organization (HUGO), and was elected to the American Society for Clinical Investigation (ASCI). He is a member of the Bioethics Advisory Committee (BAC), a national body that provides advice to the Singapore government on ethical issues related to biomedical research.
Piero Carninci, PhD
Director, Division of Genomic Technologies, RIKEN Center for Life Science Technologies

Biography
Born and Educated in Italy he obtained his doctoral degree at the University of Trieste in 1989. From 1990 to 1995 he developed technologies for DNA extraction and DNA sequencing at Talent, a spin-off biotech. He moved to Japan in 1995 at RIKEN, Tsukuba Life Science center and became tenure researcher in 1997. He has been developing technologies to capture full-length cDNAs, which were used for the construction of the Fantom projects. Between 2008 and 2013, he was a Team and Unit Leader and a Deputy Project Director at the RIKEN Omics Science Center in Yokohama. He has developed technologies to analyze the the transcribed part of the genome (transcriptome), such as the cap-trapper and the CAGE. These technologies have been broadly used in the RIKEN Fantom projects and allowed identifying non-coding RNAs as are the major output of the mammalian genome and providing comprehensive maps of the mammalian promoters. Additionally he developed a miniaturization of CAGE, in order to approach biological problems that for which there is limited amount of starting material. From April in 2013, he is a Director of the Division Genomics Technologies and a Deputy Director of Center for Life Science Technologies, RIKEN. He has published more than 200 papers and book chapters, edited books and is a member of editorial boards of various scientific journals.
Živana Težak, PhD
Associate Director for Science and Technology, Office of In Vitro Diagnostics and Radiological Health (OIR), CDRH, U.S. Food and Drug Administration

Biography
Živana Težak, Ph.D., is an Associate Director for Science and Technology, Personalized Medicine Staff, in the Office of In Vitro Diagnostic Device (IVD) Evaluation and Safety (OIR), at the Center for Devices and Radiological Health, Food and Drug Administration (FDA). Prior to joining the FDA in 2004, as a scientific reviewer in microbiology, genomics and molecular biology, Dr. Težak worked in biotechnology industry, holding research and development scientist positions in a bioinformatics and array developer company. Dr. Težak received a Ph.D. in Biochemistry/Molecular Biology from Florida State University in 1997. From 1998 to 2001 she was a research fellow at the University of Pittsburgh Medical Center and Children's National Medical Center, Research Center for Genetic Medicine, working on neuromuscular disorders, human genetics, gene therapy, and high-throughput screening technologies. Her work resulted in a number of publications in peer-reviewed journals, book chapters and proceedings. In her current position, Dr. Težak has been leading efforts to develop flexible regulatory policies for novel technology based IVDs, such as chromosomal microarrays and next-generation sequencing, in order to enable their smoother translation into the clinic.
C Jimmy Lin, MD, PhD, MHS
Founder, President, CEO, TED Fellow, Rare Genomics Institute Washington University in St. Louis

Biography
Jimmy Lin, MD, PhD, MHS, is a 2012 TED Fellow and Founder & President of Rare Genomics Institute, the world's first platform to enable any community to leverage cutting-edge biotechnology to advance understanding of any rare disease. Partnering with 18 of the top medical institutions, such as Harvard, Yale, Johns Hopkins, and Stanford, RGI helps custom design personalized research projects for diseases so rare that no organization exists to help. Dr. Lin is also a medical school faculty member at the Washington University in St. Louis and led the computational analysis of the first ever exome sequenching studies for any human disease at Johns Hopkins. He has numerous publications in Science, Nature, Cell, Nature Genetics, and Nature Biotechnology, and has been featured in Forbes, Bloomberg, Wall Street Journal, Washington Post, and the Huffington Post.
John Quackenbush, PhD
Professor of Computational Biology and Bioinformatics, Department of Biostatistics, Harvard University, Dana-Farber Cancer Institute

Biography
John Quackenbush received his PhD in theoretical physics from UCLA in 1990. Following a physics postdoc, he received a Special Emphasis Research Career Award from the National Center for Human Genome Research to work on the Human Genome Project, spending two years at the Salk Institute and two years at Stanford University working in genomics and computational biology. In 1997 he moved to The Institute for Genomic Research (TIGR), pioneering expression analysis. He joined the Dana-Farber Cancer Institute and the Harvard School of Public Health in 2005, and works reconstruction of gene networks that drive the development of diseases. In 2012 he and Mick Correll co-Founded GenoSpace, a company that develops software tools to enable precision medicine applications. <br />
Paul Billings, MD, PhD
Chief Medical Officer, Life Technologies

Biography
Board certified internist and clinical geneticist Dr. Paul R. Billings serves as Chief Medical Officer, a new position aimed at improving patient care through expanding the use of medically relevant genomic technologies in clinical settings. Dr. Billings brings extensive expertise and clinical experience in the areas of genomics and molecular medicine. Most recently, he served as Director and Chief Scientific Officer of the Genomic Medicine Institute at El Camino Hospital, the largest community hospital in the Silicon Valley. He currently serves as a member of the United States Department of Health and Human Services Secretary's Advisory Committee on Genetics, Health and Society, where he helps shape policy in the rapidly evolving field of genomic medicine. Dr. Billings has had a distinguished career as a physician and researcher. He has been a founder or chief executive officer of companies involved in genetic and diagnostic medicine, including GeneSage, Omicia and CELLective Dx Corporation. Previously, he was senior vice president for corporate development at Laboratory Corporation of America Holdings (LabCorp). He has held academic appointments at some of the most prestigious universities in the United States, including Harvard Medical School, Stanford School of Medicine and the University of California, Berkeley, and has served as a physician at a number of medical centers throughout the country, including the University of California, San Francisco. He is the author of nearly 200 publications and books on genomic medicine. Dr. Billings holds an M.D. from Harvard Medical School and a Ph.D. in immunology, also from Harvard University.
Noam Shomron, PhD
Principle Investigator, Genome Laboratory, Tel Aviv University

Biography
Dr. Noam Shomron heads a research team which focuses on the analysis of genomic sequences and gene expression aimed at understanding human diseases. Dr Shomron trained at Massachusetts Institute of Technology (MIT, Cambridge, MA, USA) where he combined high-throughput methods with computational analysis. Dr Shomron joined Tel Aviv University's Medical School in October 2008. Dr Shomron's is highly skilled in deep (next generation) sequencing technologies, in addition to parsing and processing the sequencing output. His strength in the genomic world stems from his extensive experience and knowledge using state-of-the-art methods both experimentally and computationally. Dr Shomron's overall interest and goals lie within seeking a better understanding of the mechanisms leading to disease development. His team seeks innovative solutions to generate a significant impact through translating ideas into clinical reality. Dr Shomron is also the Director of Rare Genomics Institute's Israel branch; co-founder and Scientific Director of the Functional Genomics Laboratory at Tel Aviv University; Editor-in-Chief of ‘Genetics Research' (published by Cambridge University Press); Editor of ‘Deep Sequencing Data Analysis' (a ‘Methods in Molecular Biology' book series published by Springer/Humana Press), Academic Director of BioAbroad.
Kenneth Buetow, PhD, FACMI
Director of Computational Sciences and Informatics program for Complex Adaptive Systems and Professor in the School of Life Sciences, Arizona State University

Biography
Dr. Ken Buetow is a human genetics and genomics researcher who leverages computational tools to understand complex traits such as cancer, liver disease, and obesity. Dr. Buetow currently serves as Director of Computational Sciences and Informatics program for Complex Adaptive Systems at Arizona State University (CAS@ASU) and is a professor in the School of Life Sciences in ASU's College of Liberal Arts and Sciences. CAS@ASU applies systems approaches that leverage ASU's interdisciplinary research strengths to address complex global challenges. The Computational Sciences and Informatics program is developing and applying information technology to collect, connect, and enhance trans-disciplinary knowledge both within ASU and across the broader knowledge-generating ecosystems. CAS@ASU is creating a Next Generation Cyber Capability to address the challenges and opportunities afforded by "Big Data" and the emergence of 4th Paradigm Data Science. This capability brings state-of-the-art computational approaches to CAS@ASU's transdisciplinary, use-inspired research efforts Dr. Buetow previously served as the Director of the Center for Biomedical Informatics and Information Technology within the National Institutes of Health's National Cancer Institute (NCI). In that capacity he initiated and oversaw the NCI's efforts to connect the global cancer community through community-developed, standards-based, interoperable informatics capabilities that enable secure exchange and use of biomedical data. Buetow designed and built one of the largest biomedical computing efforts in the world. He was responsible for coordinating biomedical informatics and information technology at the NCI. The NCI center he led focused on speeding scientific discovery and facilitated translational research by coordinating, developing and deploying biomedical informatics systems, infrastructure, tools and data in support of NCI research initiatives.
Pinar Bayrak-Toydemir, MD, PhD
Associate Professor, Department of Pathology, University of Utah, Medical Director, Molecular Genetics and Genomics ARUP Laboratories

Biography
Dr. Bayrak-Toydemir is a Medical Director of the Molecular Genetics and Genomics Laboratories at Associated Regional and University Pathologists (ARUP) Laboratories and an Associate Professor of Pathology at the University of Utah, School of Medicine. Dr. Bayrak-Toydemir received her MD from Ankara University School of Medicine in Ankara, Turkey, where she also received her PhD in Human Genetics. Subsequently, she completed her fellowship in Clinical Molecular Genetics at the University of Utah. She is board certified in clinical molecular genetics. Dr. Bayrak-Toydemir has a long term interest in identification of genes that cause various inherited vascular malformations. Specifically, she is interested in hereditary hemorrhagic telangiectasia, capillary malformation-arteriovenous malformation syndrome, and aortopathies. She has extensive experience on both the clinical and research applications of the next generation sequencing technology. Under her leadership Molecular Genetics Laboratory is able to offer a long list of gene panels and exome sequencing, and help to improve patient management in various disorders, by providing a comprehensive evaluation of the underlying genetic background.
Howard J Jacob, PhD

Founding Director of the Personalized Medicine Program and Human and Molecular Genetics Center, Warren P. Knowles Chair of Genetics, Professor, Department of Physiology & Pediatrics, Medi
Edward Ki Yun Leung, PhD
Clinical Chemistry Postdoctoral Fellow, University of Chicago

Biography
Born and raised in Vancouver, British Columbia, Canada. I received my Bachelor of Science and my Doctor of Philosophy from the Department of Molecular Biology and Biochemistry at Simon Fraser University. I studied the photochemistry and reduction-oxidation chemistry of nucleic acids with Dr. Dipankar Sen. I was a postdoctoral fellow for three years with Dr. Joseph Piccirilli from the Department of Biochemistry and Molecular Biology at the University of Chicago and studied RNA structural biology using phage-display technology and crystallography. For the past two years, I am in the clinical chemistry postdoctoral fellow at the University of Chicago Medicine, a ComACC certified training program under the directorship of Dr. Jerry Yeo. My research interest is in personalized medicine. My research interest is in personalized medicine. I am interested in developing and using mass spectrometry to study an observed phenotype (ie. protein levels, protein post-translational modifications, and active drugs and/or its metabolites) and next-generation sequencing to study the corresponding genotype. By combining genetic and phenotypic data, a more well-rounded and complete understanding of personalized medicine can be achieved.
John Mattick, PhD,AO, FAA, FRCPA
Executive Director, Garvan Institute of Medical Research, Conjoint Professor in the St Vincent's Hospital Clinical School and the Faculty of Medicine, at the University of New South Wale

Biography
John joined the Garvan Institute as the Executive Director in January 2012. He has made a significant contribution to the understanding of genetics and genomics through his farsighted theories on 'junk' DNA, the large non-coding sections of the human genome that do not code for proteins. Most recently John was the Professor of Molecular Biology and NHMRC Australia Fellow at the Institute for Molecular Bioscience, University of Queensland. John was educated at St Patrick's College Strathfield, the University of Sydney and Monash University, where he obtained his PhD. He has subsequently worked at Baylor College of Medicine in Houston, the CSIRO Division of Molecular Biology in Sydney, and the University of Queensland, where he was based from 1988-2011. He has also spent research periods at the Universities of Cambridge, Oxford, Cologne and Strasbourg. He was Foundation Director of the Australian Genome Research Facility and the Institute for Molecular Bioscience.
Marcel Dinger, MSc (hons), PhD
Head of Clinical Genomics, Garvan Institute of Medical Research, Conjoint Associate Professor at the University of New South Wales

Biography
Marcel Dinger is the Head of Genome Informatics at the Garvan Institute of Medical Research and conjoint Associate Professor at UNSW Australia. After completing his PhD at the University of Waikato (New Zealand), he was awarded a NZ FoRST Postdoctoral Fellowship to join Professor Mattick's group at The University of Queensland to study the role of long noncoding RNAs in mammalian development and disease. He was recruited to the Garvan Institute in 2012.
William C Nierman, PhD
Professor, Director, Infectious Diseases Program, J. Craig Venter Institute (JCVI)

Biography
Dr. William Nierman is the Director of the Infectious Disease Program at the J. Craig Venter Institute (JCVI). He is also a Professor the George Washington University School of Medicine and has taught Human Genetics at The Johns Hopkins University. He received his BS degree from the US Naval Academy and his PhD degree from the University of California, Berkeley. Dr. Nierman has broad experience in microbial pathogen genomics. His research focus is the genomic and functional analysis of two the levels of pathogen interaction with the human host, that caused by severe acute disease-causing bacterial pathogens, and that caused by fungi that can cause disease only in an immune-system-compromised host. Burkholderia mallei and Burkholderia pseudomallei are severe bacterial pathogens that cause difficult to diagnose but very life threatening diseases, glanders and melioidosis. At the other end of the pathogenicity scale are Aspergillus and Penicillium fungal pathogens which cause invasive or systemic disease in immune compromised or immune suppressed human hosts. Management of the disease in both classes of infections is becoming increasingly compromised by the rapid evolution of drug resistance in the pathogens. Both groups of organisms pose serious public health issues in both developed and in developing countries.
Bruce R Korf, MD, PhD
Professor and Chair, Department of Genetics, Director, Heflin Center for Genomic Sciences, UAB

Biography
Dr. Korf is Wayne H. and Sara Crews Finley Chair in Medical Genetics, Professor and Chair of the Department of Genetics, Director of the Heflin Center for Genomic Sciences at UAB, and Co-Director of the UAB-HudsonAlpha Center for Genomic Medicine. He is a medical geneticist, pediatrician, and child neurologist, certified by the American Board of Medical Genetics (clinical genetics, clinical cytogenetics, clinical molecular genetics), American Board of Pediatrics, and American Board of Psychiatry and Neurology (child neurology). Dr. Korf is past president of the Association of Professors of Human and Medical Genetics, past president of the American College of Medical Genetics and Genomics, and current president of the ACMG Foundation for Genetic and Genomic Medicine. He has served on the Board of Scientific Counselors of the National Cancer Institute and the National Human Genome Research Institute at the NIH. He chairs the Medical Advisory Committee of the Children's Tumor Foundation and serves on the CTF Board of Directors. His major research interests are molecular diagnosis of genetic disorders and the natural history, genetics, and treatment of neurofibromatosis. He serves as principal investigator of the Department of Defense funded Neurofibromatosis Clinical Trials Consortium. He is co-author of Human Genetics and Genomics (medical student textbook, now in fourth edition), Medical Genetics at a Glance (medical student textbook, now in third edition), Emery and Rimoin's Principles and Practice of Medical Genetics (now in 6th edition), and Current Protocols in Human Genetics.
Michael F Berger, PhD
Assistant Professor in the Department of Pathology, Research Scientist, Memorial Sloan-Kettering Cancer Center

Biography
Michael Berger, PhD is an Assistant Attending in the Department of Pathology and an Affiliate Member of the Human Oncology and Pathogenesis Program, with expertise in cancer genomics and computational biology. His research focuses on the enumeration of the spectrum of genetic mutations in human tumors in order to identify biomarkers of cancer progression and drug response. Dr. Berger joined the MSKCC faculty in October 2010 after working as a research scientist and computational biologist in the Cancer Program at the Broad Institute of Harvard and MIT. At the Broad, he served as the project leader and primary data analyst for numerous efforts employing massively parallel "next generation" sequencing to characterize genetic mutations in a range of cancers. He now runs an independent research laboratory at MSKCC that is developing methods to reliably and accurately profile clinical specimens for cancer-related DNA mutations and copy number alterations. His laboratory is engaged in many collaborations with clinical and translational investigators to discover significant oncogenic mutations in rare or understudied tumor types and identify genomic biomarkers exhibiting correlations with clinical outcomes and therapeutic response. He is also working closely with the CLIA compliant Diagnostic Molecular Pathology Laboratory to build a robust profiling pipeline and analytical framework for use in real-time patient management. Dr. Berger received his Bachelor's Degree in Physics at Princeton University and his Ph.D. in Biophysics at Harvard University.
Michael Snyder, PhD
Professor and Chair, Genetics, Director, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine

Biography
Michael Snyder is the Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. Dr. Snyder received his Ph.D. training at the California Institute of Technology and carried out postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has developed many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-of-the-art "omics" technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a cofounder of several biotechnology companies, including Protometrix (now part of Life Tehcnologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.
Christopher I Amos, PhD
Associate Director for Population Sciences, Professor of Community and Family Medicine at the Geisel School of Medicine, Norris Cotton Cancer Center, Dartmouth College

Biography
Dr. Amos moved in September, 2012 to the Geisel School of Medicine, where he is leading the Center for Genomic Medicine and serving as the Associate Cancer Center Director for Population Studies. Dr. Amos is leading studies to identify genetic risk factors for lung cancer and melanoma risk using genome-wide association and sequencing approaches. Dr. Amos leads a U19 grant entitled Transdisciplinary Research in Cancer of the Lung (TRICL) to identify genetic factors for lung cancer and interactions with smoking, study these factors in cell biological and animal models and to perform epidemiological studies of gene and environmental contributions to lung cancer risk. This grant includes 16 subcontracts and integrates work from an international consortium. Dr. Amos has served as the leader of the biostatistics core for the Genetic Epidemiology of Lung Cancer Consortium (GELCC) since its inception. With the move to Dartmouth he has replicated the computing environment that manages studies for GELCC and TRICL. Dr. Amos also provides direction for a grant that characterizes and sequences nicotinic receptors and uses fMRI to investigate effects of nicotinic receptor variants on responses to smoking cues. Dr. Amos has also worked extensively in the genetic epidemiology of colon cancer. He developed a Peutz-Jeghers syndrome registry while at M.D. Anderson Cancer Center. He has also studied genetic risk factors for sporadic colon cancer and hereditary nonpolyposis colon cancer. Dr. Amos has developed novel statistical approaches for gene-environment interaction analysis and for the identification of genes influencing complex diseases using either association based approaches or genetic linkage analysis.
Linnea Baudhuin, PhD, DABMG
Co-director, Pharmacogenomics and Genetics Laboratory, Co-director, Cardiovascular Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic

Biography
Dr. Baudhuin is Assistant Professor of Laboratory Medicine and Pathology, with a joint appointment in the Department of Medical Genetics, at the Mayo Clinic in Rochester, MN. Dr. Baudhuin is a co-director of molecular genetics, pharmacogenetics, and cardiovascular testing laboratories at the Mayo Clinic. Dr. Baudhuin received her Ph.D. in Clinical Chemistry from Cleveland State University (in conjunction with the Cleveland Clinic) and followed that up with fellowship training in Clinical Chemistry and Clinical Molecular Genetics at the Mayo Clinic. Dr. Baudhuin is board certified in Clinical Molecular Genetics by the American Board of Medical Genetics. Dr. Baudhuin's research interests lie primarily in the areas of cardiovascular-related genetics and pharmacogenetics. Dr. Baudhuin was the recipient of the 2011 Outstanding Scientific Achievements by a Young Investigator (American Association for Clinical Chemistry); the 2010 Clinical Laboratory Sciences Distinguished Author Award (American Society of Clinical Laboratory Science); and the 2006 George Grannis Award for Excellence in Research and Scientific Publication (National Academy of Clinical Biochemistry).
Matthew Lebo, PhD, FACMG
Instructor of Pathology, BWH and Harvard Medical School, Assistant Laboratory Director and Senior IS Domain Specialist Laboratory for Molecular Medicine, Partners HealthCare Center for Perso

Biography
Matthew Lebo is a trained computational biologist and ABMG-certified clinical molecular geneticist whose work focuses on using statistical and algorithmic approaches to analyze high-throughput data and to bridge genetics with computational and IT systems. Dr. Lebo is currently an Instructor of Pathology at Harvard Medical School and Brigham and Woman's Hospital, where he is developing pipelines to implement whole-genome sequencing data as a clinical test, including methods to analyze, interpret, and report identified genetic variation. Dr. Lebo serves as an Assistant Laboratory Director at the Laboratory for Molecular Medicine (LMM) and as a Senior IS Domain Specialist, both within the Partners Center for Personalized Genetic Medicine (PCPGM). As a director in a clinical diagnostics laboratory, he is responsible for the interpretation and reporting of large gene panel tests - with a special focus in cardiomyopathy - and the development of next-generation sequencing tests, including clinical genome/exome sequencing. As a member of the IT team at PCPGM, Dr. Lebo also works on the development of GeneInsight Suite, an innovative software platform for molecular laboratories, clinics, and EHR systems that manages variant, gene, and disease annotations and the integration of that information into patient reports.
George Church, PhD
Professor of Genetics, Director of the Center for Computational Genetics, Harvard Medical School

Biography
Professor of Genetics, Harvard Medical School, Director of the Center for Computational Genetics. 1984 Harvard PhD included the first direct genomic sequencing method, molecular multiplexing tags, which lead to automation & software used at Genome Therapeutics Corp. for the first commercial genome sequence -- pathogen, Helicobacter in 1994. This multiplex solid-phase sequencing evolved into polonies (1999), ABI-SOLiD (2005) & open-source Polonator.org (2007). Innovations in DNA reading, writing & allele replacement in cells lead to current research & commercialization in human genomics (Complete Genomics, PersonalGenomes.org, 23andme, Knome) , synthetic biology (SynBERC, Joule, LS9) & new ethics/security strategies.
Andrew Hessel, MSc
Distinguished Research Scientist, Autodesk Inc., Faculty, Singularity University

Biography
Autodesk Distinguished Research Andrew Hessel excels at building bridges and catalyzing change. He is a trend-spotter in life science and helps individuals and organizations better understand and prepare for a future of accelerating innovation. He is also the co-founder of the Pink Army Cooperative, the world's first cooperative biotechnology company, which is aiming to produce open source viral therapies for cancer. Trained in microbiology and genetics, Andrew has continually worked at the forefront of genomics, first to read and comprehend bacterial, human, and other genomes and more recently to write them. He believes the technology that makes this possible, know as synthetic biology, is revolutionary and that it will eventually surpass information technology (IT) as an economic engine and driver of societal change. He is an advocate of open source genetic engineering and sees DNA technologies growing to resemble the software industry as they continue to evolve. He speaks widely on topics that include cells as living computers, life science as an emerging digital industry, and biological safety and security.
Agnieszka Lichanska, PhD
Laboratory Director, TessArae, LLC

Biography
She obtained her PhD at the University of Queensland in Australia in a field of biochemistry, and subsequently worked as a post-doctoral fellow at Queen's University of Belfast, University of Queensland and Institute for Molecular Biosciences. Since 2005 until 2008 she held a continuing appointment as a lecturer in a School of Dentistry at the University of Queensland and established her own laboratory in area of functional genomics and metabonomics. She has over 10 years of experience in molecular biology, genetics, genomics, biochemistry, microbiology and metabonomics. In addition she has experience as a science writer. Recently Agnieszka served on the Council of the Australian Society for Biochemistry and Molecular Biology and is still active in the society. Currently she is working on novel diagnostic assays for infectious diseases using microarray re-sequencing technology.
Alisa Jackson, Zach Smith, Mary Blair, Dave Delano
Alisa Jackson, Moderator, Beckman Coulter, Inc. Zach Smith, MS, Project Scientist, The Center for Genomics and Bioinformatics, Indiana University Mary Blair, Senior Application Scientist,

Biography
Zach Smith serves as the next generation sequencing and laboratory automation specialist at the Center for Genomics and Bioinformatics at Indiana University, Bloomington. His duties include the construction of sequencing libraries for Illumina and Roche 454 sequencing platforms as well as the development of new automation protocols for NGS and genomics research. Mary Blair helps scientists address their automated sample preparation challenges. Mary is responsible for internal development of automated methods for popular Genomic sample preparation kits and protocols on Beckman Coulter's Biomek liquid handling platforms. These fully supported Biomek sample preparation methods are for popular applications such as NGS and qPCR. Fully implemented they yield consistent, quality samples at an increased throughput with decreased labor. Dave Delano manages products in Illumina's gene expression and regulation portfolio including RNA-seq, ChIP-Seq, and methylation applications.
Charles Cantor, PhD
Chief Scientific Officer, Sequenom

Biography
Dr. Charles Cantor is a founder, and Chief Scientific Officer at SEQUENOM, Inc., which is a genetics discovery company with tools, information and strategies for determining the medical impact of genes and genetic variations. He is also the founder of SelectX Pharmaceuticals, a drug discovery company, Retrotope, an anti-aging company, and DiThera, a biotherapeutic company. Dr. Cantor is professor emeritus of Biomedical Engineering and of Pharmacology and was the director of the Center for Advanced Biotechnology at Boston University. He is currently adjunct professor of Bioengineering at UC San Diego, adjunct professor of Molecular Biology at the Scripps Institute for Research, and distinguished adjunct professor of Physiology and Biophysics at UC Irvine. Prior to this, Dr. Cantor held positions in Chemistry and then in Genetics and Development at Columbia University and in Molecular Biology at the University of California at Berkeley. Cantor was educated in chemistry at Columbia College (AB) and at the University of California Berkeley (PhD). Dr. Cantor has been granted more than 60 US patents and, with Paul Schimmel, wrote a three-volume textbook on biophysical chemistry. He also co-authored the first textbook on Genomics titled 'The Science and Technology of the Human Genome Project'. In addition, he sits on the advisory boards of numerous national and international biotechnology firms, has published more than 450 peer-reviewed articles, and is a member of the U.S. National Academy of Sciences.
Yaniv Erlich, PhD
Principal Investigator, Andria and Paul Heafy Family Fellow, MIT Whitehead Institute for Biomedical Research

Biography
Dr. Yaniv Erlich is Andria and Paul Heafy Family Fellow and Principal Investigator at the Whitehead Institute for Biomedical Research. He received a bachelor's degree from Tel-Aviv University at Israel and his PhD from the Watson School of Biological Sciences at Cold Spring Harbor Laboratory in 2010. Dr. Erlich's research interests are computational human genetics. His research featured in the New York Times, Wall Street Journal, and NPR. Dr. Erlich is the recipient of the Harold M. Weintraub award, the IEEE/ACM-CS HPC award, Wolf Foundation Scholarship for Excellence in Exact Sciences, and he was selected as one of 2010 Tomorrow's PIs team of Genome Technology.
Jessica C Mar, PhD
Assistant Professor, Department of Systems & Computational Biology, Assistant Professor, Department of Epidemiology & Population Health, Albert Einstein College of Medicine

Biography
Jessica Mar is an Assistant Professor at the Albert Einstein College of Medicine in the Department of Systems and Computational Biology in the Bronx, New York. The Mar lab investigates how variability of gene expression informs our understanding of how genes and pathways are dysregulated in disease. Dr. Mar received her PhD in Biostatistics from Harvard University in 2008. Previously she was a postdoctoral research fellow at the Dana-Farber Cancer Institute in Boston and a visiting scientist at the European Bioinformatics Institute in the United Kingdom. She is a recipient of a University of Queensland medal and an American-Australian Fulbright award. She is currently an Associate Editor of Genomics.
Daniel Caffrey, PhD
Assistant Professor at the University of Massachusetts Medical School, Program Chair for the Bioinformatics Program, Instructor in the Rabb School of Continuing Studies, Division of Graduate

Biography
Daniel Caffrey is an Assistant Professor in the Department of Medicine at UMASS Medical School. He is also the Program Chair of Bioinformatics at Brandies University. He received his Ph.D from Trinity College Dublin where he studied the evolution and function of the MAP kinase pathways. He completed his postdoctoral training at Pfizer before spending several years there as a Computational Biologist. His current research interests include genome evolution and host-pathogen interactions.
Steven Rosenberg, PhD
Chief Scientific Officer, CardioDx, Inc.

Biography
Steven Rosenberg joined CardioDx in 2006 and is responsible for the scientific staff and for research and development programs in the areas of genomics, genetics, and informatics. In addition, Steven is currently on the Board of Directors of KMT Hepatech. Prior to joining CardioDx, Steven served for three years as the Chief Scientific Officer of XDx, Inc., a molecular diagnostics company focused on diseases of the immune system. He led the group responsible for developing AlloMap, a molecular diagnostic for heart transplant patients, the first genomics-based test in transplant immunology. Prior to XDx, Steven spent a year as a consultant and visiting scholar at the University of California, Berkeley. From 1981 to 2001 he was at Chiron Corporation, where he was named one of only three Chiron Research Fellows in the company's history. He received his Ph.D. in biochemistry from the University of California, Berkeley, and is the author of more than 40 scientific publications, and an inventor of more than 20 U.S. patents.
Patrice Milos, PhD
Chief Executive Officer, Claritas Genomics

Biography
Dr. Milos recently joined Claritas Genomics, a newly formed company focused on pediatric molecular diagnostics emerging from Boston Children's Hospital in partnership with Life Technologies. Claritas Genomics combines the power of next-generation DNA sequencing technology with the clinical expertise of the world's best pediatric specialists to inform and improve patient care. Patrice most recently served as the Boston Site Head for Pfizer's Centers of Therapeutic Innovation and Precision Medicine Lead. The CTI model represented a new and exciting approach to drug discovery through establishment of academic medical center partnerships, including Beth Israel, Boston Children's Hospital, Tufts Medical Center, Boston University School of Medicine and Partners Healthcare, along with Pfizer to establish proof of mechanism for novel targets and pathways aiming to treat human disease. Dr. Milos previously served as the Senior Vice President and Chief Scientific Officer for Helicos BioSciences Corporation, Cambridge, MA joining in June 2007. Her expertise and extensive knowledge in the life sciences helped advance the company's efforts to develop and apply innovative and breakthrough single molecule DNA and RNA sequencing technology with recent focus on molecular diagnostics. Accomplishments included the development of the world's first and only method for direct capture and sequencing of BRCA1/2, the only method for direct sequencing of RNA as well as the establishment of collaborations with world class institutions including the Broad Institute, Harvard Medical School, Massachusetts General Hospital and the Children's Oncology Group. Patrice's previously served as Executive Director for Pfizer Global Research and Development, Groton, CT. Patrice was responsible for leadership, strategy alignment and execution of the scientific disciplines of pharmacogenomics, proteomics, metabonomics and RNA profiling applied across the Pfizer portfolio from early discovery into the marketplace. Initially joining Pfizer in 1993, Dr. Milos held numerous research positions of increasing responsibility focusing on Cardiovascular and Metabolic Disease, Pharmacogenomics, DNA Sequencing, Biomarkers and Molecular Sciences. Dr. Milos serves on the Boston Children's Hospital Technology Advisory Board, is an active NIH grant reviewer and has served on the National Advisory Council for Human Genome Research. Patrice was also pivotal in the establishment and oversight of key Pfizer strategic investments in the genomics area, most notably, the Genetic Association Information Network in partnership with NIH. She also sits on several journal editorial boards and has published and presented extensively in genomic sciences. Dr. Milos conducted post-doctoral fellowships at Brown University and Harvard University. She earned her MS and PhD degrees at Rensselaer Polytechnic Institute in Troy, NY.
Nir Barzilai, MD
Director, Institute for Aging Research, Ingeborg and Ira Leon Rennert Chair in Aging Research, Professor, Department of Medicine (Endocrinology), Professor, Department of Genetics, Albert Ein

Biography
Dr. Barzilai is the Director of the Institute for Aging Research at the Albert Einstein College of Medicine and the Director of the Glenn Center for the Biology of Human Aging and of the Nathan Shock Center of excellence in biology of aging. He is The Ingeborg and Ira Leon Rennert Professor of Aging Research, Professor of Medicine and Molecular Genetics and a member of the Diabetes Research Center, the Divisions of Endocrinology and Geriatrics. Dr. Barzilai's interests focus on several basic mechanisms in the biology of aging, including the biological effects of nutrients on extending life and the genetic determinants of life span. Indeed, he has discovered longevity genes in humans, and is further characterizing the phenotype and genotype of humans with exceptional longevity through an NIH supported Program Project. He received numerous grants, among them ones from the National Institute of Aging (NIA), American Federation of Aging Research, and the Ellison Medical Foundation. Dr. Barzilai has published over 200 peer-reviewed papers, reviews and chapters in textbooks. He is an advisor to the National Institutes of Health on several projects and initiatives and study sections (currently on NIA-Biology). He serves on several editorial boards and is a reviewer for numerous other journals. Dr. Barzilai was a recipient of numerous prestigious awards, including the Beeson Fellow for Aging Research, the Senior Ellison Foundation award, the Paul Glenn Foundation award and the NIA- Nathan Shock Award and the recipient of the 2010 Irving S. Wright Award of Distinction in Aging Research Award.
Nathan R Treff, PhD
Director of Molecular BiologyResearch, Reproductive Medicine Associatesof New Jersey, Associate Professor, Department of Obstetrics, Gynecology,and Reproductive Sciences, UMDNJ-Robert Wood Jo

Biography
Dr. Nathan Treff serves as Director of Molecular Biology Research at RMA of New Jersey, Associate Professor at the Robert Wood Johnson Medical School, and Adjunct Professor at Rutgers University. Dr. Treff's laboratory uses molecular genetics to discover, develop, and translate novel molecular diagnostics to improve the quality of life for patients with infertility and has published more on the use of arrays in preimplantation aneuploidy screening than any other group in the world. His research was awarded the 2007 and 2010 General Program Prize and the 2009 and 2010 Society for Assisted Reproductive Technology Prize by the American Society for Reproductive Medicine. He completed his Ph.D. in biochemistry at Washington State University where he earned the Charles Glenn King Scholarship and the National Institutes of Health Predoctoral Fellowship in protein biotechnology. Dr. Treff trained as a postdoctoral fellow in stem cell biology at the University of Wisconsin-Madison, and in reproductive biology at the EMD-Serono Research Institute.
Bruce K Patterson, MD
CEO and Founder, IncellDx Inc

Biography
Dr. Patterson received his undergraduate training in molecular biology from the University of Michigan in Ann Arbor. He then went on to Northwestern University Medical School for training in medicine. During the early stages of the AIDS epidemic, Dr. Patterson began investigating cellular reservoirs of HIV-1 using molecular and in situ technology patented in his laboratory. Dr. Patterson went on to a residency in Pathology focusing on viral pathogenesis. While in his residency, Dr. Patterson determined that enough HIV virus was present in infected individuals to account for the massive destruction of the immune system. This paradigm altering work was published in Science in 1993. Dr. Patterson later was named Chief Resident of Pathology at Northwestern Memorial Hospital. Dr. Patterson has authored over 100 manuscripts and book chapters and he continues his work on HIV-1 pathogenesis and reservoirs at Stanford University School of Medicine. Dr. Patterson was the Medical Director of Diagnostic Virology at Stanford University Hospitals and Clinics.
Vincent P Mauro, PhD
Associate Professor of Neurobiology, Scripps Institute

Biography
Dr. Mauro is an Associate Professor in the Department of Neurobiology at the Scripps Research Institute in La Jolla, California. He is also a co-founder and lead scientist of Promosome, a biotechnology company focused on bioproduction enablement and DNA vaccines. In addition, Dr. Mauro is a Senior Fellow in Experimental Neurobiology at the Neurosciences Institute in San Diego, California. Prior to moving to The Scripps Research Institute, Dr. Mauro received his Ph.D. at McGill University in Montreal, Quebec, and continued his studies as a postdoctoral fellow at The Rockefeller University in New York City. Dr. Mauro studies both fundamental and applied aspects of translational control mechanisms. His basic research is focused on understanding how eukaryotic mRNAs recruit ribosomes, how ribosomes subsequently locate initiation codons, and how ribosomes regulate the translation of specific subsets of mRNAs. Dr. Mauro's applied studies build on his basic research. These applied studies have led to the identification of Translational Enhancer Elements (TEEs) and the generation of synthetic translational enhancers.
Kimberly Strong, PhD
Assistant Professor, Primary Faculty for the Program in Genomics and Ethics, Medical College of Wisconsin

Biography
Kimberly Strong, PhD is the primary faculty with the Program in Genomics and Ethics at the Medical College of Wisconsin's Center for Bioethics and Medical Humanities and she also holds a secondary appointment with the MCW Human and Molecular Genetics Center. She has degrees in Biology, Genetic Counseling, and Bioethics and has direct experience in preimplantation genetic diagnosis, embryology, genetic counseling, psychosocial research, patient advocacy and research ethics and her lectures have included bioethical issues related to assisted reproductive technologies, gamete donation, genetic counseling, genetic testing and stem cell research. Dr. Strong's broad academic area of expertise is in the application and limits of 'empirical bioethics', particularly its value in informing the discourses surrounding contentious and emerging technologies. Her current research revolves around exploring the ethical and social issues involved in the use of whole genome sequencing.
Robert Roberts, MD, FRCPC, MACC, LLD (Hon.)
President, Chief Executive Officer and Chief Scientific Officer, Professor of Medicine, Director, Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute

Biography
Robert Roberts is the President and CEO of the University of Ottawa Heart Institute and founding Director of The Ruddy Canadian Cardiovascular Genetics Centre. He received his M.D. from Dalhousie University and completed his residency in Internal Medicine and Fellowship in Cardiology at the University of Toronto. Funded by a Canadian Heart Foundation Scholarship, he pursued research in heart disease and in 1982 became Chief of Cardiology at Baylor College of Medicine in Houston, Texas. As a cardiologist, educator and scientist, he developed the MCBK Test which has been used to diagnose heart attacks for the past three decades. Dr. Roberts' research led him to molecular biology and genetics, during which time he discovered many genes responsible for heart disease. Dr. Roberts is generally regarded as one of the founders of molecular cardiology. Dr Roberts has had a distinguished and prolific career as a Cardiologist, Educator and Scientist having published over 850 scientific articles and received many awards including the 2012 Research Achievement Award from the Canadian Cardiovascular Society; the 2012 Distinguished Fellowship Award from the International Academy of Cardiology; the McLaughlin Medal from the Royal Society of Canada and the Albrecht Fleckenstein Memorial Award from the International Academy of Cardiology in 2008; Citation for Highly Cited Researcher from ISI Thomson Scientific in 2002; and the Distinguished Scientist Award from the American College of Cardiology in 1998.
David F Keren, MD
Professor, Department of Pathology, Associate Director, Clinical Pathology Laboratories, University of Michigan Health System

Biography
Dr. Keren received his B.S., M.S. and M.D. degrees from the University of Illinois, the latter in 1971. He completed his residency training in Anatomic and Clinical Pathology and postdoctoral training in Immunopathology and Immunohematology at The Johns Hopkins Hospital from 1971-1976. From 1976-1978 he served as a Major in the United States Armed Forces at the Walter Reed Army Institute for Research in Washington, D.C. He joined the Department of Pathology of the University of Michigan in 1978. From 1989 through 2011 he served as the Medical Director of Warde Medical Laboratory while continuing as an Adjunct Clinical Professor of Pathology at the University of Michigan. Dr. Keren has authored over 160 peer-reviewed articles and has written or edited 13 books. He has received several awards including the Carl A. Jolliff Award from the Clinical and Diagnostic Immunology Division of the American Association of Clinical Chemists, a Lifetime Achievement Award from the Michigan Society of Pathologists, the Israel Davidsohn Award, the Distinguished Service Award, and the Mastership Award from the American Society for Clinical Pathology. Dr. Keren served as the President of the Gastrointestinal Pathology Society (1993), President of the Michigan Society of Pathologists (2000), President of the American Society for Clinical Pathology (2003), and President of the American Board of Pathology (2011). Currently, he is a Trustee of the American Board of Pathology and a member of the CAP Hematology and Clinical Microscopy Resource Committee.

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