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Maternal Dietary Factors and Whole-Exome Sequencing of Primary Congenital Glaucoma and Anterior Segment Defects of the Eye

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Maternal Dietary Factors and Whole-Exome Sequencing of Primary Congenital Glaucoma and Anterior Segment Defects of the Eye MATERNAL DIETARY FACTORS AND WHOLE-EXOME SEQUENCING OF PRIMARY CONGENITAL GLAUCOMA AND ANTERIOR SEGMENT DEFECTS OF THE EYE Kristin Jean Voltzke A dissertation submitted to the faculty at the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Epidemiology. Chapel Hill 2019 Approved by: Andrew F. Olshan Suzan L. Carmichael Tania A. Desrosiers Kari E. North Robert E. Meyer © 2019 Kristin Jean Voltzke ALL RIGHTS RESERVED ii ABSTRACT Kristin Jean Voltzke: Maternal Dietary Factors and Whole-Exome Sequencing of Primary Congenital Glaucoma and Anterior Segment Defects of the Eye (Under the direction of Andrew F. Olshan) There are few studies on the risk factors of primary congenital glaucoma (PCG) and anterior segment defects (ASDs) of the eye in a US-based population. The goal of this dissertation was to evaluate maternal diet, a modifiable risk factor, and to explore genes which have not previously been evaluated within PCG cases. Each of these exposures were evaluated within the National Birth Defects Prevention Study (NBDPS), a large population-based case- control study in the United States. Specific Aim 1 evaluated maternal diet through intake levels of individual micronutrients, a diet quality score, and the creation and evaluation of dietary patterns. Inverse, albeit imprecise, associations were seen for a number of individual micronutrients. Diet quality did not appear to be associated with having a child with PCG or ASDs. Mothers who adhered to the Prudent and Mexican dietary patterns appeared to have lower odds of having a child with these defects. In Specific Aim 2, samples from a subset of PCG cases from the NBDPS underwent whole-exome sequencing. The goal of this aim was to identify rare mutations in genes which previously have not been investigated in relation to PCG. We found a similar proportion (13.5%) of families with variants in CYP1B1, the most commonly mutated gene in PCG. In addition, we found a number of variants present in individual families which occurred in genes that are known to underly other Mendelian conditions, some with phenotypic iii overlap, or genes which are known to play a role in eye development signaling pathways. These genes, and specific variants, should be further explored through in vitro, in vivo, and other epidemiologic studies to better understand the genetic mechanisms in PCG cases. The findings of this dissertation add to the sparse literature on risk factors for PCG and ASDs. iv I would like to dedicate this work to my family for their constant encouragement and to my amazing fiancé, Patrick Moore, for your continuous love and support. v ACKNOWLEDGMENTS First and foremost, I would like to express my appreciation to the women and families who participated in the National Birth Defects Prevention Study and the study staff at each center without whom this work would not be possible. I would also like to thank the members of the North Carolina Center of the National Birth Defects Prevention Study, the University of Washington Center for Mendelian Genomics, and Mary Jenkins and Lynn Almli at the CDC for their helpful feedback and support of this work. Finally, I would like to express my most sincere gratitude to my dissertation committee for their guidance and encouragement throughout the dissertation process. vi TABLE OF CONTENTS LIST OF TABLES ......................................................................................................................... ix LIST OF FIGURES ........................................................................................................................ x LIST OF ABBREVIATIONS ........................................................................................................ xi CHAPTER 1 – INTRODUCTION AND SPECIFIC AIMS .......................................................... 1 CHAPTER 2. - BACKGROUND ................................................................................................... 5 2.1 Development of the eye and associated structures ............................................................... 5 2.2 Congenital Glaucoma ........................................................................................................... 8 2.3 Risk Factors of primary and congenital glaucoma and anterior chamber defects ........................................................................................................................ 15 2.4 Maternal diet ....................................................................................................................... 21 2.5 Section 2 summary .............................................................................................................. 23 CHAPTER 3. – STUDY DESIGN AND METHODS ................................................................. 24 3.1 Study overview ................................................................................................................... 24 3.2 National Birth Defects Prevention Study ............................................................................ 24 3.3 Methodology for Specific Aim 1 ........................................................................................ 27 3.4 Methodology for Specific Aim 2 ........................................................................................ 36 CHAPTER 4. – MATERNAL DIET AS A RISK FACTOR FOR PRIMARY CONGENITAL GLAUCOMA AND DEFECTS OF THE ANTERIOR SEGMENT OF THE EYE ........................................................................ 42 4.1 Introduction ......................................................................................................................... 42 4.2 Materials and Methods ........................................................................................................ 44 vii 4.3 Results ................................................................................................................................. 47 4.4. Discussion .......................................................................................................................... 54 CHAPTER 5. – EXOME SEQUENCING TO IDENTIFY NOVEL GENES UNDERLYING PRIMARY CONGENITAL GLAUCOMA IN THE NATIONAL BIRTH DEFECTS PREVENTION STUDY. ........................................... 59 5.1 Introduction ......................................................................................................................... 59 5.2 Materials and Methods ........................................................................................................ 60 5.3 Results ................................................................................................................................. 62 5.4. Discussion .......................................................................................................................... 68 CHAPTER 6. – DISCUSSION AND CONCLUSIONS .............................................................. 76 6.1 Summary of Specific Aims ................................................................................................. 76 6.2 Strengths and Limitations ................................................................................................... 78 6.3 Public Health Implications and Future Studies ................................................................... 80 6.4 Conclusions ......................................................................................................................... 81 APPENDIX 1. SUPPLEMENTARY TABLES FOR CHAPTER 4 ............................................ 83 Supplemental Table 1. ORs and 95% CIs for individual nutrients for combined primary congenital glaucoma and anterior segment defects, stratified by periconceptional vitamin use .................................................................................... 83 Supplemental Table 2. ORs and 95% CIs for individual nutrients, stratified by case group status ....................................................................................................... 87 REFERENCES ............................................................................................................................. 91 viii LIST OF TABLES Table 2.1. Diagnostic Criteria for types of congenital glaucoma ................................................... 8 Table 3.1. Response rates by PCG and ACDs by center and total. .............................................. 26 Table 3.2. Variables and planned initial coding schemes for confounders in Aim 1. .................. 34 Table 3.3. List of micronutrients evaluated for associations with PCG and ASDs. .................... 35 Table 3.4 Filters used in determination of candidate variants using different models of inheritance. ................................................................................................................... 39 Table 4.1. Demographic and clinical characteristics of primary congenital glaucoma and anterior segment defect cases and controls, National Birth Defects Prevention Study, 2000-2011. ......................................................................................... 50 Table 4.2. ORs and 95% CIs for individual nutrients for combined primary congenital glaucoma and anterior segment defects, National Birth Defects Prevention Study, 2000-2011........................................................................................................ 52 Table 4.3 Association between dietary pattern class and having a child with primary congenital
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