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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.