ASSESSING THE NON-GENETIC AND GENETIC FACTORS AFFECTING REFRACTION IN THE AGING ADULT POPULATION by Samantha Bomotti A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, MD January, 2018 ©2018 Samantha Bomotti All Rights Reserved Abstract Refractive errors are the most common form of visual impairment in the world, and are becoming an increasing public health burden as the world’s population ages. Refractive errors arise from changes in the shape of the eye, such as axial length and corneal curvature, or from aging of the lens. Refraction is a quantitative trait underlying refractive errors. The goal of this project was to investigate the non-genetic and genetic factors affecting refraction, a complex multifactorial trait, in the aging adult population. We used phenotypic data available from the population-based Beaver Dam Eye Study (BDES) consisting of 4,972 individuals aged 43-86 years at baseline to identify and characterize the association of nuclear sclerosis, among other factors, with refraction and changes in refraction. We then imputed exome array data in a subset of BDES participants to enhance our coverage of protein-coding regions and identify variants associated with refraction or either of its biological determinants, axial length and corneal curvature. Finally, we conducted a heritability analysis to determine whether the heritability of refraction varied by nuclear sclerosis severity, and to quantify the genetic or environmental influences shared between refraction and nuclear sclerosis. We determined nuclear cataract is the primary contributor to the myopic shift observed in older persons, as only those with nuclear cataract experienced a myopic shift while those without nuclear cataract did not. Sex, diabetes, and baseline refractive error, but not education, were also associated with refractive changes. While we were unable to detect novel genetic loci associated with refraction, axial length, or corneal curvature, we demonstrated that variants associated in prior studies are also associated with these same phenotypes in the BDES, validating these genetic variants as contributors to the etiology ii of these phenotypes. Finally, the heritability of refraction was consistent across differing distributions of nuclear sclerosis severity, and approximately one third to one half of the genetic effects contributing to refraction and nuclear sclerosis were shared. The results of these studies can help better characterize the underlying etiology of refraction for improved preventative measures and targeted treatments designed to counteract the development of refractive errors in older persons. Advisors: Dr. Priya Duggal, PhD Dr. Alison P. Klein, PhD Thesis Readers: Dr. Priya Duggal, PhD Dr. Alison P. Klein, PhD Dr. Joan Bailey-Wilson, PhD Dr. Ingo Ruczinski, PhD iii Acknowledgements I want to begin by thanking my high school chemistry professor, Mrs. Viscardo. Her passion and enthusiasm for chemistry, and encouragement to pursue science in my own future, directed my own path toward science in college and graduate school. To this day I consider her the best teacher I ever had. I would also like to thank my MPH advisor, Dr. Sharon Kardia, for her diligent mentorship during my tenure at the University of Michigan. Her patience, wisdom, and good humor were invaluable as I navigated my way through my very first genetic epidemiology project, from which I gained an even greater appreciation and enthusiasm for the field. Of course, My PhD would not be possible without the superior mentorship I received during my time at Johns Hopkins. Firstly, I want to thank Dr. Robert Wojciechowski for always being so kind and approachable to me, particularly when I was a new student and knew few others in the program. I also sincerely appreciate his persistent collaboration with other researchers on my behalf, and how he facilitated networking opportunities for me, when I was first searching for a project. Dr. Terri Beaty has remained a consistently reliable, honest, and truly supportive mentor throughout my tenure at Johns Hopkins. I have deeply valued her wisdom and support and would not have navigated through the program nearly as smoothly without her. My Thesis Committee members, Dr. Bryan Lau, Dr. Alison Klein, and Dr. Priya Duggal, undoubtedly deserve my gratitude for dedicating so much of their time to frequent (and often long) meetings with me, to reading through drafts of my material, and iv steering me in the right direction when I began to go of course. Their guidance has made me a more confident and better epidemiologist, and I cannot thank them enough for the endless amount of support and direction they provided to bring me to where I am now. My primary advisor in particular, Dr. Duggal, deserves a round of applause for meeting with me weekly and responding to my needs in such a timely manner in spite of her incredibly busy schedule. I sincerely thank all of my oral exam committee members (Dr. Chris Ladd- Acosta, Dr. Priya Duggal, Dr. Elizabeth Platz, Dr. Rasika Mathias, Dr. Alison Klein, Dr. Bryan Lau, and Dr. Elizabeth Colantuoni) for their time and for their positive encouragement before and during my oral exams. I also want to give a special thank you to Dr. Colantuoni, who met with me several additional times after I passed my oral exams to discuss my project and offer expert advice regarding my statistical methods. Her patience and kindness, and constant willingness to answer any questions I had no matter how busy she was with her own students, meant a great deal to me and certainly helped advance my own abilities as an epidemiologist. I appreciate her dedication. I was honored during my tenure to be offered a TA and Lead TA position by Drs. Amber D’Souza and Stephan Ehrhardt. Their confidence in my abilities as a teacher, and as an epidemiologist, helped convince me of my own abilities. My experiences as TA and Lead TA under their skilled and passionate guidance will be considered among my best and most fulfilling experiences at Johns Hopkins. I owe such a debt of gratitude to Fran Burman and Matt Miller, without whom I would have been completely lost. They simply know everything about everything related to the department. I never once asked them a question they could not answer. They were v constantly my allies and always worked in my best interest, for which I cannot thank them enough. They also acted as in-house counselors during stressful times. I am convinced all students would be completely lost without them and my experience here was definitely enhanced by my interactions with them. All of my professors, Thesis readers, and any faculty who had a positive influence on my education while I was at Johns Hopkins absolutely deserve my sincerest gratitude for their diligence, effort, and dedication to the education and well-being of all of their students, including me. There are simply too many individuals who have improved my experience here in some way to name, but I want them all to know that I appreciate all they did and do for all of us. Most importantly, I want to thank my family and friends. I would have no emotional support system without them, and I certainly would not have survived graduate school without their ardent love and support. I especially want to thank my parents. I would not be where I am or who I am without them. They have given me everything I have and everything I could ever need or want. Their unwavering confidence in me, even when I had none in myself, has allowed me to get to where I am. I am incredibly lucky to have such supportive and loving parents who have dedicated so much of their time and energy to my progress and well-being. Finally, I have to thank my fiancé Tim. Tim is my closest confidant, best friend, and greatest source of happiness. Regardless of anything else going on, he has never failed to make me smile with his words of comfort and sense of humor. His unconditional love and support, even during the most challenging times, has become a persistently shining light in my life that has provided me with the strength necessary to face each day and achieve my goals. vi TABLE OF CONTENTS Abstract .......................................................................................................................... ii Acknowledgements ........................................................................................................ iv CHAPTER ONE Introduction and Specific Aims Refraction and Refractive Errors ...................................................................................... 2 The Burden of Refractive Errors in an Aging Population ................................................. 7 Overview of the Project ................................................................................................... 7 Aim 1: Non-Genetic Factors Affecting Refraction and Changes in Refraction in Older Adults ............................................................................................................................ 10 Aim 2: Genetic Factors Affecting Refraction in Older Adults ........................................ 13 Aim 3: Shared Genetic and Environmental Effects of Refraction and Nuclear Sclerosis ................................................................................... 16 Thesis Organization ....................................................................................................... 17 References ....................................................................................................................