GENETIC VARIATION IN THE DOMESTICATED DOG AS A MODEL OF HUMAN DISEASE DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Jennie Lynn Rowell, M.S. Graduate Program in Nursing The Ohio State University 2012 Dissertation Committee: Donna O. McCarthy, Adviser Carlos E. Alvarez, Cognate Adviser Kim McBride Jodi McDaniel i ii Copyright by Jennie Lynn Rowell 2012 iii ABSTRACT One of the greatest challenges facing clinical scientists is a developed understanding of the genetic basis for complex human diseases such as cancer. Despite many technological advances in genetics, progress has been slow. This is owed, in part, to intricate gene-gene interactions as well as poorly understood environmental influences on gene expression and genetic traits. The high level of heterogeneity of the human genome makes identification of these interactions and environmental influences difficult. Recently, the domesticated dog (Canis Lupis Familaris), has demonstrated its powerful applicability to human disease as a new model of genetic variation. Dogs are an excellent model for the study of complex disease in humans for a variety of reasons, including the extensive level of health care they receive, and their phenotypic diversity. Approximately 400 inherited diseases similar to those of humans are characterized in dogs, including complex disorders such as cancers, heart disease, and neurological disorders. The purpose of this dissertation project is to elucidate the role of genetic variation in the domesticated dog as a model for understanding human disease and is comprised of four manuscripts. I establish 1) the utility of the canine model for the study of human disease, 2) the theoretical and empirical establishment of a novel method for genomewide genetic analysis, 3) identification of germline loci associated with the risk for development of Osteosarcoma. Finally, 4) I describe a novel mechanism involving structural variation iv which results in an epigenetic readout for a highly penetrant Mendelian trait. I discuss how each of these studies stands to broadly accelerate biomedical investigation. v DEDICATION This document is dedicated to the people who supported me in following my dreams. vi ACKNOWLEDGEMENTS I would like to express my deepest gratitude to the individuals who, through their support and encouragement, made this dissertation project possible both academically and personally. First, I would like to thank my both my nursing and cognate advisers. Dr. Donna McCarthy helped me to develop my scientific career goals. She demanded my best efforts, and in return devoted countless time and effort to provide support, including additional assertiveness when needed. Dr. Carlos Alvarez allowed me to learn and work in his genetics lab when I had no prior experience. He was incredibly patient and kind in his teaching, providing me with a strong basis on which to build my understanding of genetics. He allowed me to participate in countless activities that strengthened my skills as a future principle investigator. To both of them, I am completely indebted for the investment they made in me. I would like to thank my committee members, Drs. Kim McBride and Jodi McDaniel. Dr. McBride provided much support the statistical understanding of this project, including assisting in manuscript preparation and principle dialogue that helped to shape this project. Although joining my dissertation committee near the end of the project, Dr. McDaniel provided insightful comments and questions to spur critical thinking and generous encouragement. vii I would also like to acknowledge all of the faculty and staff at The Ohio State University College of Nursing, and The Research Institute at Nationwide Children’s Hospital Center for Human & Molecular Genetics for their assistance on many technical aspects of these experiments, and willing providing assistance. I would like to recognize Dr. C. Guillermo Couto, Dr. Sara Zaldivar-Lopez, and Dr. Lilian Marin for sample collection, clinical expertise, and support of this work. Working with them demonstrates the heart of collaborative research. I would also like to Leszek Rybaczyk, Elise Fiala, and Fortune Shea. These members of my lab assisted me throughout this project with technical aspects of this work, as well as challenged me to further develop my computational and analytical skills. I would like to personally acknowledge many friends who have become family, Dr. Anjel (Pook) Stough-Hunter and Nikki Seagraves, who through their constant support and encouragement, made this process easier. I would also like to recognize Gloria Zender, Tracey Edwards, Cassie Span, Shannon Schlagbaum, Valerie Brown, Deb Osborn, Jackie Crouthers, Marni Dunlap, Heather Osborn, and Joel Brummel who provided much needed support which enabled to complete this aspect of my education. I would also like express my immense debt of gratitude to Beth McKee and Abbey Carter-Logan. Without their kindness, generosity, example, and ability to see what my future could be, I would not have been able to achieve any of my dreams academically or personally. I would like to thank my family, whose critical role is often played behind the scenes of such an accomplishment. I thank my grandparents (Alex and Emily Marzek) for viii all of their love and support. I thank my parents (Dean and Betsy Rowell) for helping to shape my aspirations, teaching me to love learning at an early age and allowing me to pursue my dreams through their own personal sacrifice. I thank my mother (“mumso”), for her unconditional love, constant encouragement, and especially for reminding me “this too shall pass”. I thank Amy and Brian Newby, for their unconditional love, reassurance, and sense of humor. I also thank my brother, who as my roommate was possibly most effected during the last months of completing this process. I appreciate his love, encouragement, and support. Lastly, this work would not have been possible without the grace of Jesus Christ. I have been blessed with an amazing support system professionally and personally. ix VITA 2001................................................................Diploma, Rowell Homeschool 2005................................................................B.S. Nursing, Cedarville University 2009................................................................M.S. Nursing Research, College of Nursing, The Ohio State University PUBLICATIONS Rowell JL, McCarthy DO, Alvarez CE. Dog models of naturally occurring cancer. Trends Mol Med. 2011 Mar 23. PMID: 21439907. Rowell, J.L. & Blakely, W.P. (2008). Discussion questions in Pathophysiology: Concepts of altered health states, 8th Ed. Edited by Carol Porth. Philadelphia: Lippincott, Williams & Wilkins. FIELD OF STUDY Major Field: Nursing x TABLE OF CONTENTS ABSTRACT.........................................................................................................................IV DEDICATION .....................................................................................................................VI ACKNOWLEGDMENTS..................................................................................................... VII VITA ..................................................................................................................................VII TABLE OF CONTENTS .......................................................................................................XI LIST OF TABLES.............................................................................................................XIII LIST OF FIGURES ..............................................................................................................XV CHAPTER 1:INTRODUCTION............................................................................................... 1 CHAPTER 2: DOG MODELS OF NATURALLY OCCURRING CANCER ................................. 5 CHAPTER 3: GENOMEWIDE INTERSECTION-UNION ANALYSIS (GIA) INCREASES THE POWER TO DETECT GENETIC ASSOCIATIONS ................................................................ 29 CHAPTER 4: USE OF GENOMEWIDE INTERSECTION-UNION ANALYSIS IDENTIFIES RISK LOCI FOR CANINE OSTEOSARCOMA ............................................................................... 62 CHAPTER 5: GENETIC AND MOLECULAR MECHANISMS OF A MENDELIAN TRAIT WITH EPIGENETIC READOUT: CANINE BRINDLE COAT PATTERN ........................................... 137 xi Materials and Methods................................................................................................ 171 CHAPTER 6: CONCLUSION ............................................................................................. 177 REFERENCES................................................................................................................... 180 xii LIST OF TABLES CHAPTER 3: GENOMEWIDE INTERSECTION-UNION ANALYSIS (GIA) INCREASES THE POWER TO DETECT GENETIC ASSOCIATIONS Table 3.1. Comparison of published GWA results and GIA reanalysis for four traits in LUPA data..................................................................................................................... 57 Table 3.2. QTL of size .................................................................................................. 61 CHAPTER 4: USE OF GENOMEWIDE INTERSECTION-UNION ANALYSIS IDENTIFIES RISK LOCI FOR CANINE OSTEOSARCOMA Table 4.1. Phenotype information of Greyhounds used in this study ........................ 106 Table 4.2.