Biotechnology and Bioinformatics Symposium (BIOT-2012)

Lynn Vogel, Ph.D.

Associate Professor, Department of Bioinformatics and Computational Biology,
Chief Information Officer,
UT MD Anderson Cancer Center,
Houston, TX

Bioinformatics and Clinical Care: The Challenges of Bridge-Building

Scientific discovery has its own rewards, as does the clinical care of patients. However, increasingly scientists (and bioinfomaticians in particular) are being expected to pursue courses of inquiry that are not judged by their "own rewards" but by their potential impact on the lives of patients. The intersection of biology and computer science is being challenged with the expectation that what we discover in the end must make a difference--not only in improving our understanding of how biological processes work, but in making an impact on these processes so that the lives of people with diseases like cancer can be changed. For the individual cancer patient, the goal is nothing less than extending timeline of life itself. There are significant challenges to these expectations, and in this presentation, Dr. Vogel will focus on four of them: 1) the volume of data we need to work with; 2) the challenge of validating what we are doing; 3) the sheer complexity of the tasks at hand; and 4) the challenge of dealing with the academic silos that have historically characterized the process of scientific discovery to the clinical impact of the science.

Biography:

Lynn H. Vogel, Ph.D., is Vice President and Chief Information Officer at The University of Texas MD Anderson Cancer Center (UT-MDACC) in Houston, Texas, an integrated clinical, research and teaching institution that is the world's largest and consistently one of the highest rated facilities devoted to the prevention, care and cure of cancer.

In 2006, under Dr. Vogel's leadership, MD Anderson was named to the CIO 100 list of the most innovative information technology (IT) organizations, to the top 100 of InformationWeek's Top 500, has been honored twice as one of the top 25 connected healthcare facilities by Health Imaging and IT, and named as the inaugural recipient of the Transformation Leadership Award, which is sponsored jointly by the College of Healthcare Information Management Executives (CHIME) and the Center for Healthcare Transformation. In 2007, Dr. Vogel was named as one of Computerworld's Premier 100 IT Leaders, and was awarded a "Best in Class" for his contributions to healthcare IT. In 2010, MDACC was again honored by Computerworld as a leader in the healthcare information technology by designation as a Laureate, and also by awarding the institution its prestigious 21st Century Achievement Award in Healthcare. In 2011, Dr. Vogel was recognized by InformationWeek magazine as a member of the InformationWeek Healthcare CIO 25, a select group of individuals identified as "leading the healthcare IT revolution".

Dr. Vogel also has an appointment as Associate Professor of Bioinformatics and Computational Biology at UT-MDACC, and carries an adjunct appointment in Management at The University of Texas School of Public Health. Dr. Vogel has also held faculty and IT leadership appointments at The University of Chicago, The City University of New York and Columbia University.

Funda Meric-Bernstam, M.D.

Professor, Department of Surgical Oncology,
Medical Director, Institute of Personalized Cancer Therapy,
UT MD Anderson Cancer Center,
Houston, TX

Personalized Cancer Therapy: Promises and Challenges

Evolution in biotechnology has made high-throughput characterization of tumors possible. Nextgen sequencing has made genomic analysis affordable. At the same time, new targeted therapies are rapidly becoming available. Thus, we can finally deliver the promise of personalized therapy. However, even highly-specialized physicians at leading academic centers are not equipped to apply the molecular and genomic information available in publically available sources to clinical-decision-making concerning individual patients. There is a great need for researchers from all disciplines to collaborate in order to leverage the rapidly accumulating information gained from genome sequencing, functional genomics, transcriptomics, proteomics, among others. We will review some of the recent successes in personalized cancer therapy, as well as specific challenges to biomarker discovery, molecular therapeutics and truly personalized therapy with an emphasis for opportunities for collaboration.

Biography:

Funda Meric-Bernstam is a Professor of Surgical Oncology at the University of Texas MD Anderson Cancer Center in Houston, Texas. She is also a member of the University of Houston at Texas Graduate School of Biomedical Sciences Faculty.

Dr. Meric-Bernstam has recently been named the Medical Director of the MD Anderson Cancer Center Institute of Personalized Cancer Therapy. She is leading several exciting initiatives such as the unusual responder program -an institution-wide biomarker discovery effort. She is also spearheading institution-wide efforts to incorporate somatic mutation analysis into patient care and to develop decision support tools.

Dr. Meric-Bernstam graduated Cum Laude from Yale University School of Medicine in 1991 and completed her residency in general surgery at the University of Michigan Medical Center in 1998. In her third year of residency, she joined the National Institute of Health as a postdoctoral fellow. After completing her general surgery residency, she did a surgical oncology fellowship at the University of Texas MD Anderson Cancer Center. After fellowship, she joined MD Anderson's faculty in 2001 as a surgeon-scientist. In 2005, Dr. Meric-Bernstam received the Outstanding Teaching Award for Research from the Department of Surgical Oncology at MD Anderson Cancer Center. She is the Principal Investogator of the T32 fellowship program "Training Academic Surgical Oncologists."

Dr. Meric-Bernstam has been the PI /co-PI on several clinical trials and translational studies focused on biomarkers. She has been the chair of one of the clinical research committees at MD Anderson. Dr Meric-Bernstam is the recipient of the 2009 Society of Surgical Oncology Clinical Investigator Award funded by Susan G. Komen for the Cure. She is the MD Anderson lead for clinical trials in the AACR Stand Up to Cancer Dream team on PI3K in Women's Cancers.

Dr. Meric-Bernstam has authored over 190 peer-reviewed articles in journals such as Journal of Clinical Oncology, Cancer Research, Clinical Cancer Research, Molecular Cancer Therapeutics, Annals of Surgery and Annals of Surgical Oncology. She has also written chapters for more than 20 books. Dr Meric-Bernstam has given numerous lectures internationally and is committed to enhancing cancer care globally.

David Wheeler, Ph.D.

Associate Professor, Department of Molecular and Human Genetics
Human Genome Sequencing Center,
Baylor College of Medicine

Second Generation Sequencing in Cancer Genomes

Next generation sequencing instruments are producing DNA sequence at an ever increasing rate. The Human Genome Sequencing Center will sequence the genomes of over 10,000 patients across a wide variety of diseases in 2012, about a third of those will be cancer. Processing and analyzing the massive amounts raw sequencing data required to analyze each patient's cancer presents enormous challenges. This talk will examine the challenges and the solutions in place today, and show how this enterprise will revolutionize cancer treatment in the not-too- distant future.

Biography:

David A. Wheeler received Bachelor of Science degrees in biochemistry and zoology from the University of Maryland and a Master of Science in biochemistry from the George Washington University. He received his Ph.D. in Molecular Genetics from the George Washington University with his dissertation in mouse models of human cancer. Dr. Wheeler did postdoctoral research in behavioral genetics at Brandeis University. He successfully transfered the courtship song rhythm of D. simulans to D. melanogaster by creating transgenic melanogaster carrying the simulans period gene. Through this work he became interested in the new field of bioinformatics. He joined the laboratory of Charles Lawrence in 1991, at Baylor College of Medicine, to develop computational tools for molecular biology. He directed the Molecular Biology Computation Resource at Baylor College of Medicine for 10 years and in 2001 he joined the Human Genome Sequencing Center at BCM. In the HGSC, Dr. Wheeler guided the finishing of the D. melanogaster chromosome 3 and X genome sequence in 2002, followed by the human genome sequence, chromosomes 3, and 12, in 2003. Dr. Wheeler is now the Director of Cancer Genomics, and Assitant Director of the HGSC. He leads the development of methods for discovery of genome variation in human and animal populations using DNA sequencing technologies with the goal of relating polymorphism to human disease.

Wayne D. Newhauser, Ph.D.

Dr. Charles M. Smith Chair of Medical Physics,
Professor and Director, Medical Physics and Health Physics,
Department of Physics & Astronomy,
Louisiana State University

High Performance Computing for Proton Radiation Therapy

Predictions of exposure to charged particle radiation are commonly performed for patients receiving radiotherapy. This presentation will review the physical and computational approaches to predict radiogenic toxicity in these patients. The discussion will include a brief overview of the sources of radiation exposure and how these vary with host and treatment factors. Modeling approaches discussed will including algorithms to predict radiation dose and radiogenic risk for the development of second cancers, including the application of Monte Carlo methods and supercomputing techniques. The review will conclude with a brief summary of currently available dose computing capabilities, unmet needs, and possible directions for future research.

Biography:

Dr. Newhauser's research focuses on heavy particle dosimetry calculations and measurements. After receiving degrees in nuclear engineering and medical physics at the University of Wisconsin, he worked as a post-doctoral fellow and staff scientist at the German National Standards Laboratory (PTB, Braunschweig), an assistant professor at Harvard Medical School and Massachusetts General Hospital, and a tenured associate professor of radiation physics at The University of Texas M. D. Anderson Cancer Center. Currently, Prof. Newhauser serves as director of the graduate program in medical physics at Louisiana State University and Chief of Physics at the Mary Bird Perkins Cancer Center, both in Baton Rouge. In his current position, he teaches and leads a research group that investigates advanced radiotherapies, radiation effects, and cancer survivorship. Dr. Newhauser is also a board certified, licensed, and practicing medical physicist. He is active in several professional and scientific societies and serves in leadership roles in the American Association of Physicists in Medicine and the American Nuclear Society.

Randall Splinter, Ph.D.

HPC Solution Architect,
Hewlett-Packard

High Performance Computing in the Biological Sciences

High performance computing (HPC) is the application of large supercomputers or large clusters of computers to problems of scientific and engineering interest. In many fields of science and engineering HPC has become a third pillar in addition to theoretical and experimental studies. In those cases computer simulations can help provide insight into problems that may be too expensive, too slow, too difficult or too dangerous to study using traditional experimental techniques. Additionally, in some cases the explosive growth of data has forced the use of HPC to analyze experimental data and to implement non-traditional data management solutions to cope with the rapid growth of data. I will provide a brief overview of the history of HPC, where we currently are and finally some of the problems that are looming on the horizon.

Like many fields of science the biological sciences have started to draw heavily on HPC. Similar to many problems in HPC the biological sciences have brought their own sets of issues and requirements that are pushing the envelope of what is possible today and driving future technology development. For instance, the application of radiation physics techniques for the study of radiation/tissue interaction has driven the growth of very large core-count compute clusters, while next generation sequencing has much more modest computational requirements, but is forcing the industry to study more scalable data management solutions to accommodate the explosive growth of data that the next gen sequencers produce. In this last half of the presentation I will summarize how HPC has impacted several biological sub-disciplines to drive better and faster scientific outcomes.

Biography:

Dr. Randall Splinter started with Hewlett-Packard in 1997. Prior to working at Hewlett-Packard he spent two years at the University of Kentucky's Center for Computational Sciences as a Postdoctoral Scholar where he performed research in computational cosmology. His Ph.D. is from the University of Kansas where he studied computational and theoretical astrophysics. While at Kansas he spent three years as a NASA Graduate Student Research Fellow and participated in summer schools in high performance computing at the Pittsburgh Supercomputer Center and at NASA Goddard Space Flight Center. Dr. Splinter has published research work in the fields of cosmology and large-scale structure formation, general relativity and particle astrophysics.

Dr. Splinter has worked in the area of high performance computing for approximately 20 years. His work at Hewlett-Packard has focused on architecting high performance computing solutions for Hewlett-Packard customers. He currently works for the ISS America's Hyperscale Group at Hewlett-Packard.