Symposium Tuesday, May 12, 2015 10:00 a.m. – 6:30 p.m. Jackson Center • Huntsville, Alabama PRESENTED BY: AGENDA 09:30 a.m. – 10:00 a.m. Registration and Refreshments 10:00 a.m. – 10:20 a.m. Introduction to HudsonAlpha Richard M. Myers, Ph.D., HudsonAlpha Institute for Biotechnology and Co-Director of the UAB-HudsonAlpha Center for Genomic Medicine 10:20 a.m. - 10:40 a.m. Introduction to UAB-HudsonAlpha Center for Genomic Medicine Bruce R. Korf, M.D., Ph.D., University of Alabama at Birmingham and Co-Director of the UAB-HudsonAlpha Center for Genomic Medicine 10:40 a.m. – 11:00 a.m. (HA + UAB) = Move-to-Alabama Haydeh Payami, Ph.D., University of Alabama at Birmingham and HudsonAlpha Institute for Biotechnology 11:00 a.m. – 11:20 a.m. Sequencing and Genomics Capabilities at HudsonAlpha Shawn E. Levy, Ph.D., HudsonAlpha, Director of the Genome Sequencing Laboratory 11:20 a.m. – 12:00 p.m. Tour of the HudsonAlpha Facility 12:00 p.m. – 01:00 p.m. Lunch 01:00 p.m. – 01:20 p.m. Combination of Bioinformatics Expertise at HudsonAlpha with Clinical Expertise at UAB for Genetic Diagnosis of Developmental Disorders Greg M. Cooper, Ph.D., HudsonAlpha Faculty 01:20 p.m. – 01:40 p.m. Current Collaborations with HudsonAlpha on Epigentics Hemant K. Tiwari, Ph.D.,University of Alabama at Birmingham, Statistical Genetics 01:40 p.m. – 02:00 p.m. Genomic and Epigenomic Analysis of Disorders and Diseases in Collaboration with University of Alabama at Birmingham Devin M. Absher, Ph.D., HudsonAlpha Faculty 02:00 p.m. – 02:30 p.m. Break 02:30 p.m. – 03:30 p.m. Dialogues with the Experts HudsonAlpha Faculty Investigators and Senior Scientists 03:30 p.m. – 03:50 p.m. Integrated Genomic and Metabolomic Analysis Reveals Key Metabolic Pathways in Pancreatic Cancer Sara J. Cooper, Ph.D., HudsonAlpha Faculty 03:50 p.m. – 04:10 p.m. Genetics, Genomics and Autoimmune Disease Robert P. Kimberly, M.D., University of Alabama at Birmingham, Center for Clinical and Translational Science (CCTS) 04:10 p.m. – 04:30 p.m. Genomics and Epigenomics of Levodopa-Induced Dyskinesia in Parkinson Disease David G. Standaert, M.D., Ph.D., University of Alabama at Birmingham 04:30 p.m. – 06:30 p.m. Reception SPEAKERS Richard M. Myers, Ph.D. President and Science Director HudsonAlpha Institute for Biotechnology Dr. Myers is the President and Science Director of the HudsonAlpha Institute for Biotechnology and co-director of the UAB-HudsonAlpha Center for Genomic Medicine. He received his Ph.D. in Biochemistry from the University of California Berkeley and has more than 35 years of experience studying the regulation of gene expression, human genetics and genomics. He directed one of the first U.S. genome centers starting in 1990, and has been involved in applying functional genomics and genetics approaches to understand how genes and regulatory regions contribute to basic biology, human disease, responses to environment and population genetics. Dr. Myers’ Laboratory uses DNA sequencing and other high-throughput methods to identify genetic variants and to develop and apply technologies to measure DNA sequence variation, gene expression, microRNA and other non-coding RNA expression, epigenetic events and binding of transcription factors to their sites in the genome on a comprehensive, whole-genome level. They have applied these approaches towards understanding brain diseases, several types of cancer, including — pancreatic, colon, prostate, breast and kidney cancer — immune-mediated inflammatory disorders and differential responses to drugs in clinical trials. The Myers Laboratory, along with the other faculty at HudsonAlpha, collaborate with many groups around the world. Bruce Korf, M.D., Ph.D. Wayne H. and Sara Crews Finley Chair of Medical Genetics Professor and Chair, Department of Genetics Director, Heflin Center for Genomic Sciences University of Alabama at Birmingham Dr. Korf completed his undergraduate studies and M.D. at Cornell University and received his Ph.D. in Genetics and Cell Biology from Rockefeller University. He then did training in pediatrics, child neurology and genetics at Children’s Hospital, Boston, and is board certified in all three areas, as well as clinical cytogenetics and clinical molecular genetics. He is the Wayne H. and Sara Crews Finley Chair in Medical Genetics, chair of the Department of Genetics and director of the Heflin Center for Genomic Sciences. He also is co-director of the UAB-HudsonAlpha Center for Genomic Medicine. Dr. Korf is the past president of the Association of Professors of Human and Medical Genetics and of the American College of Medical Genetics and Genomics and is the 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 of the National Human Genome Research Institute at the NIH. Dr. Korf is the author of Human Genetics and Genomics, co-author of Medical Genetics at a Glance, and co-editor of Current Protocols in Human Genetics and Emery and Rimoin’s Principles and Practice of Medical Genetics. His research focuses on the genetics and treatment of neurofibromatosis type 1, and he also has a major interest in genetics and genomics education and the integration of genetics into medical practice. He directs the UAB Undiagnosed Diseases Program, which provides diagnostic assessments including genome sequencing for children and adults with chronic undiagnosed conditions. Haydeh Payami, Ph.D. University of Alabama at Birmingham HudsonAlpha Institute for Biotechnology The Payami Lab is working towards prevention and treatment of Parkinson’s disease. PD is not a single disease: there are a myriad of genetic and environmental factors involved. The Payami Lab is interested in the genes that interact with environmental risk factors – the goal being to predict who is at risk and what they should avoid — and also the genes that determine efficacy and toxicity of drugs for prevention and treatment, so that treatment can be personalized for maximum benefit for each individual. While they are on the fast track for effective prevention and treatment, they are also interested in gaining a deep understanding of how the disease develops, why it progresses, why it affects so many systems of the body (physical, cognitive, psychiatric, digestive) and how best to bring it to a halt. Shawn Levy, Ph.D. Director of the Genomic Services Laboratory at HudsonAlpha Institute for Biotechnology Upon his arrival at HudsonAlpha in 2009, Dr. Shawn Levy and his team developed the HudsonAlpha Genomic Services Laboratory, which supports projects using genomic technologies from laboratories around the world. Since its inception, the CLIA-certified Genomics Services Laboratory has supported more than 2,200 projects and more than 110,000 samples. Prior to joining HudsonAlpha, Dr. Levy was founding director of the Vanderbilt Microarray Shared Resource and was responsible for growing it from a small microarray core facility to a world-renowned genomics center. Dr. Levy received his graduate and postdoctoral training at Emory University School of Medicine, and his research interests include environmental — genomics including genomics of the built environment, the genetic basis of complex disease and the development and optimization of life science technology. Greg Cooper, Ph.D. HudsonAlpha Institute for Biotechnology Greg Cooper is a computational biologist focused on understanding the structures, functions and evolutionary histories of individual human genomes and finding ways to translate that understanding into useful predictions about human health and disease. He develops and applies genomic knowledge and annotations to better identify mutations with phenotypic effects, with a particular interest in genomic diagnoses for children with intellectual disabilities and developmental delays. He received a B.A. in Microbiology and a B.S. in Mathematics and Statistics from Miami University, as well as a Ph.D. in Genetics from Stanford University. He then conducted post-doctoral research at the University of Washington before moving to HudsonAlpha as a Faculty Investigator in September 2010. Hemant Tiwari, Ph.D. Head of Section on Statistical Genetics William “Student” Sealy Gosset Professor Director, Biostatistics Pre-Doctoral NHLBI Training Program Director, Post-Doctoral NHLBI Training Program in Statistical Genetics Department of Biostatistics Dr. Tiwari received his Ph.D. in mathematics from the University of Notre Dame, South Bend, Indiana. While being a faculty at the University of Maine, he got interested in statistical genetics, and completed a post-doctoral fellowship in Statistical Genetics under Prof. Robert Elston in the Department of Biometry and Genetics at Louisiana State University Medical center, New Orleans and at the Case Western Reserve University in Cleveland. Subsequently, he worked as a faculty member in the Department of Epidemiology and Biostatistics at Case Western Reserve University. In January 2002, he joined as a faculty in the Department of Biostatistics (Section on Statistical Genetics) at UAB. His research interests include Genetic Linkage Analysis, Disequilibrium Mapping, Genome-Wide Association Studies, Structural variations, Epigenetics, Pharmacogenetics/ Pharmacogenomics, gene expression, exome sequencing, pathway analysis, Bioinformatics, and Metabolomics. Currently, he is involved in gene mapping studies of immunological disorders, cardiovascular diseases, multiple sclerosis, to name few. Devin Absher, Ph.D. HudsonAlpha Institute for Biotechnology The research focus in the Absher Lab is on the application of genomics to complex diseases and traits. This has included genomewide association studies and, more recently, epigenetic studies. The Absher Lab’s projects include multiple studies of autoimmune diseases (lupus, rheumatoid arthritis), cardiovascular disease and the dietary and metabolic risk factors for heart disease. The Absher Lab also has a keen interest in aging and the effects of aging on the epigenome, as well as projects on cancer epigenetics. Sara Cooper, Ph.D. HudsonAlpha Institute for Biotechnology The Sara Cooper Lab is focused on developing technologies in metabolomics and genomics and applying them to human problems. Sara has previously developed metabolomic methods using yeast and now is applying these methods to explore human disease. Her team has completed assays of human biofluids, human tissue and tissue culture cells to characterize neurological disease, cancer and to understand fundamental questions in cellular metabolism. Their primary focus is integrating genomic and metabolomic methods to understanding the role for cellular metabolism in pancreatic cancer. They also have projects investigating whether bacterial genomes contain a key for the breakdown of pollutants and using genomics to explore the potential for a new drug in treating ovarian cancer. While Cooper’s Lab is interested in a diverse set of biological problems, it aims to use common tools (metabolomics and genomics) to solve the problems. Robert Kimberly, M.D. Howard L. Holley Professor of Medicine, Director, UAB Center for Clinical and Translational Science Dr. Kimberly is an internationally recognized translational scientist with substantial experience in the development of large, multisite and multiple-investigator scientific programs. His research group is interested in the role of genetic factors in the normal function of the immune system and in the development of autoimmune and immune-mediated inflammatory diseases, such as systemic lupus erythematosus (SLE) and systemic vasculitis. The group’s approach has focused on receptors for immunoglobulin (Fc receptors) as a model system and has explored molecular mechanisms of receptor signaling and the molecular basis for receptor polymorphisms in humans. Allelic variations in receptor structure profoundly affect receptor function. The team has been a leader in developing several national and international research consortia for the study of human diseases, and they have demonstrated that certain low-binding alleles are enriched in SLE patients. More active alleles are over-represented in patients with vasculitis and severe renal disease. In addition to identifying susceptibility alleles, these studies have led to molecular insights into responsiveness to Ig-based therapeutics. As prominent contributors in major population-based genome wide association studies, the group is also pursuing epigenetic signatures as markers for pathways in pathogenesis and for disease activity. David G. Standaert, M.D., Ph.D. John N. Whitaker Professor and Chair of Neurology University of Alabama at Birmingham Dr. Standaert graduated from Harvard College in 1982. He received his M.D. and Ph.D. degrees from Washington University in St. Louis. He completed a one-year internship in Medicine followed by a three-year Neurology residency at the University of Pennsylvania. He was appointed a Howard Hughes Medical Institute Physician Research Fellow, and completed a three-year research and clinical fellowship in Neurology (Movement Disorders) at Massachusetts General Hospital in 1995. He subsequently joined the faculty at Harvard Medical School and MGH, where he served as Director of the MGH/MIT Udall Center of Excellence in PD Research. Dr. Standaert relocated to the University of Alabama at Birmingham in July of 2006, and he is now the John N. Whitaker Professor and Chair of the Department of Neurology. He serves as Director of the Division of Movement Disorders, the Director of the APDA Advanced Center for Parkinson Research at UAB and Director of the UAB Bachmann-Strauss Center for Dystonia and Parkinson Disease. He sees patients in a weekly clinic and oversees many clinical trials for new treatments of Parkinson’s disease. He is Chair of the Scientific Advisory Board of the American Parkinson Disease Association, a member of the Scientific Advisory Board of the Michael J. Fox Foundation for Parkinson Research, an Associate Editor of the journal Movement Disorders, and a member of the Board of Directors of the American Neurological Association. He is a member of the Board of Directors of the UAB Health System and Chair of the UAB Health Services Foundation Advisory Committee. Dr. Standaert’s Laboratory works on understanding both the root causes of Parkinson’s disease as well as the origin of the disabling symptoms that appear after long term treatment of the disease. In addition to the speakers, the following scientists will join the dialogues’ session. Michelle Amaral, Ph.D. HudsonAlpha Institute for Biotechnology Dr. Amaral is a Postdoctoral Fellow in the Myers Lab at HudsonAlpha. She was originally trained in structural biology, performing x-ray crystallographic studies on proteins with therapeutic potential. Next, she obtained a Ph.D. in Neuroscience from the University of Alabama at Birmingham (UAB) where she studied the effects of brain-derived neurotrophic factor on transient receptor potential channels in the hippocampus and, ultimately, its effect on learning and memory in rat models. She also studied the balance between excitatory and inhibitory neurotransmission in mouse models of Rett syndrome. At HudsonAlpha, Dr. Amaral works on clinical sequencing and analysis of whole exome and whole genome data collected from patients who have neurodevelopmental disorders, as part of the Clinical Sequencing Exploratory Research (CSER) team; she performs similar analysis for the UAB Undiagnosed Diseases Program. Dr. Amaral also leads several projects pertaining to the analysis of sequencing data from individuals who have psychiatric disorders, such as schizophrenia and major depression. Corneliu Henegar, M.D., Ph.D. HudsonAlpha Institute for Biotechnology Dr. Henegar is a Senior Scientist and expert in bioinformatic analysis of animal and human genomes. He was trained initially as an M.D. and is specialized in internal medicine, metabolism and endocrinology. In parallel with his medical studies, he underwent extensive training in computer science and bioinformatics in undergraduate and graduate school, and he obtained his Ph.D. from Paris XIII University in 2008. He joined the Barsh Lab in 2010 as a postdoctoral fellow and has since led several analytical projects involving transcriptomic and epigenetic studies as well as whole genome sequencing of animal genomes — including dogs, wild cats, horses, cows and zebras. Susan Hiatt, Ph.D. HudsonAlpha Institute for Biotechnology Dr. Hiatt is a Senior Scientist at HudsonAlpha. In September 2014, she joined the variant analysis team, a group of scientists responsible for analysis of exome and genome sequence data to identify causal variants in individuals with a variety of distinct phenotypes for both clinical and basic research applications. Dr. Hiatt also oversees updates to data in the variant annotation pipeline, a key tool used in the identification of causal of variants. Before joining HudsonAlpha, Dr. Hiatt was a database curator in the Reference Sequence (RefSeq) group at NCBI. In addition to analysis of nucleotide and protein sequences for representation in the public RefSeq collection, she also trained new staff, aided in overall RefSeq dataflow optimization and assisted in the annotation of over 30 vertebrate genomes. She is part of the analytic team for our CSER project to identify genetic variations in children that result in developmental delay and/or intellectual disability. Marie Kirby, Ph.D. HudsonAlpha Institute for Biotechnology Dr. Kirby is a Senior Scientist in Dr. Myers’ Laboratory. Her background is in biochemistry and cell biology, and she received her Ph.D. in 2009 from Emory University in Atlanta, Georgia, in the laboratory of Dr. Maureen Powers. Her current research focus is genomic analysis of cancer in order to identify clinically relevant biomolecular signatures. She investigates whole transcriptome and epigenome signatures in pancreatic and prostate tumor tissues and adjacent-unaffected tissues to identify putative diagnostic and prognostic biomarkers for these cancers. Dr. Kirby also studies RNA expression patterns in pancreatic cell lines in order to understand the biology of chemotherapeutic response. More recently, she has been involved in a project investigating microRNA signatures in patient plasma as a mechanism for detecting disease. Brittany Lasseigne, Ph.D. HudsonAlpha Institute for Biotechnology Dr. Lasseigne is a Postdoctoral Fellow at HudsonAlpha who works in both the Myers and Cooper Laboratories. She has expertise in both the biological and computational/statistical aspects of human genetics and genomics, having made significant discoveries in the genomics of renal cell carcinoma, schizophrenia and, recently, ALS. Brian Roberts, Ph.D. HudsonAlpha Institute for Biotechnology Brian received his B.S. in Chemical Engineering from the University of California Berkeley. He spent several years working for Merck on various genomics projects, including microarray gene expression analysis, siRNA design and screening and miRNA biology. Since joining HudsonAlpha in 2012, Brian has focused on miRNA sequencing technology development and data analysis for early detection of colon cancer.
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