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Tutorial 5: Overview of and Statistical Analysis of “-omic” Data

Title: Overview of and Statistical Analysis of “-omic” Data

Presenters:
Mark Adams, Associate Professor, Department of Genetics, School of Medicine, Case Western Reserve University

Jill Barnholtz-Sloan, Assistant Professor, Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University

Mark Chance, Professor and Director, Center for Proteomics, Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

Jean-Eudes Dazard, Visiting Assistant Professor, Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University

Sunil Rao, Associate Professor, Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University

Abstract: Advancements in technology now allow for genome wide data at the genomic, epigenomic, gene expression and proteomic levels to be obtained in a relatively quick, cost effective manner.  These types of “-omic” data are now being used to classify subgroups of organisms by molecular patterns, predict outcomes from complex diseases and map genes related to a multitude of complex phenotypes.  This tutorial serves as an introduction to various types of “-omics” data, their utility and how to think about statistical analysis of these data.  We will first introduce the variety of “-omic” data types that can be generated and how they can be used.  We will then introduce some basic statistical analysis approaches to examining these data.  Then we will specifically focus on more detailed statistical analyses methods for genome-wide association, gene expression and proteomics studies. 

Biographical Sketches of Presenters:
Dr. Mark Adams received a B.A. in Chemistry from Warren Wilson College in Swannanoa, NC in 1984. He received his Ph.D. in Biological Chemistry from the University of Michigan in 1990.  As a postdoctoral fellow in the laboratory of Dr. J. Craig Venter at the National Institute of Neurological Disorders and Stroke at the NIH, Dr. Adams developed the expressed sequence tag (EST) methodology for rapid characterization of the expressed set of genes in a tissue. As one of the founding scientists at The Institute for Genomic Research, Dr. Adams established and managed the large-scale DNA sequencing facility.  He also contributed extensively to determining the first genome sequence of a free-living organism, Haemophilus influenzae, as well as to several additional microbial genomes.  In 1998, Dr. Adams co-founded Celera Genomics, where he was responsible for the DNA sequencing and genome annotation groups. In this role he directed the Drosophila, human, and mouse genome sequencing projects and the effort to re-sequence exons and regulatory regions of all human genes to identify novel functional SNPs. Dr. Adams joined the faculty of Case Western Reserve University in 2003 as an Associate Professor.  He currently works on the evolution of multidrug resistance in bacteria and on mouse models of hematopoietic defects. (Email: mda13@case.edu)

Dr. Jill Barnholtz-Sloan received her B.A. in Mathematics from University of Florida in Gainesville, Florida, in 1994 and a M.S. in Statistics from the University of Texas at Austin in 1995. She received her Ph.D. in Biostatistics/Statistical Genetics from University of Texas School of Public Health in Houston, Texas, in 2000.  Her dissertation work focused on assessing the effects of population admixture on inference for traditional linkage analysis in family data as a pre-doctoral fellow at MD Anderson Cancer Center in Houston, Texas.  Dr. Barnholtz-Sloan is multi-disciplinary trained in biostatistics, population genetics and human genetics.  Dr. Barnholtz-Sloan’s research focuses on genetic/molecular epidemiology of cancer, statistical modeling of clinical outcomes after cancer diagnosis, statically analysis of local and national cancer registry data and racial/ethnic disparities in cancer, specifically using estimates of genetic ancestry to better understand differences between groups of diseased individuals.  Dr. Barnholtz-Sloan is a co-investigator on various cancer genetic epidemiology and genome-wide association studies of brain tumors, lung cancer and ovarian cancer.  Dr. Barnholtz-Sloan joined the faculty at Case Western Reserve University School of Medicine in 2007 as an Assistant Professor in the Case Comprehensive Cancer Center. (Email: jsb42@case.edu)

Dr. Mark Chance received his bachelor’s degree in Biology from Wesleyan University and his Ph.D. degree in Biophysics from the University of Pennsylvania.  Dr. Chance furthered his training as a Postdoctoral Research Associate at AT&T Bell Laboratories.  He went on to become Assistant Professor in the Department of Chemistry at Georgetown University.  He then served as Assistant Professor at Albert Einstein College of Medicine in Bronx, New York and was soon promoted to Associate Professor of the Departments of Physiology & Biophysics and Biochemistry.  He was Professor at AECOM when he moved to the Case School of Medicine in 2005, where he is currently the Director of both the Case Center for Proteomics and Bioinformatics and Case Center for Synchrotron Biosciences and Professor of Physiology and Biophysics.  Dr. Chance is an internationally renowned scientist in the field of mass spectrometry. He is an expert in the quantitative mass spectrometry and 2-D Gel techniques that enable scientists to identify biomarkers and regulatory pathways in colon cancer, diabetes, radiation exposure, and HIV infection. (Email: mark.chance@case.edu)

Dr. Jean-Eudes Dazard received his MSc in computer science in 1992 from the graduate school of engineering (ESIM), France, and his PhD in Molecular Biology and Bioinformatics in 2000 from the University of Montpellier I (CNRS), France. He then took two years of postdoctoral training in Bioinformatics from the Weizmann Institute of Science (WIS), Israel; followed by three years in Statistics under the guidance of Dr J. Sunil Rao when he became fellow of the Computational Genomic training program, here at Case Western Reserve University. As a result, he received a second Msc in Statistics from the department of Statistics at Case Western Reserve University. Dr. Dazard joined the faculty of Case Western Reserve University in Nov. 2006 as a Visiting Assistant Professor in the Department of Epidemiology and Biostatistics, and recently accepted a position as Assistant Professor in the Center for Proteomics and Bioinformatics. (Email: jxd101@case.edu)

Dr. J. Sunil Rao  received his BSc. in Biology from the University of Ottawa and his M.S. in Biostatistics from the University of Minnesota followed by a Ph.D. in Biostatistics from the University of Toronto.  He took an Assistant Professor position at the Cleveland Clinic and then moved over to Case Western Reserve University where he is currently an Associate Professor and Director of the Division of Biostatistics.  Dr. Rao’s areas of research interest include statistical genomics and high throughput data modeling; machine learning and statistical learning theory and statistical model selection.  His areas of application focus are primarily in cancer genomics.  (Email: sunil@nalini.EPBI.cwru.edu)

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