HERITABILITY AND GENETIC DETERMINANTS OF NORMAL HUMAN FACIAL SHAPE AND BODY SIZE by JOANNE BURNETTE COLE B.S., University of Maryland, 2010 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Human Medical Genetics and Genomics Program 2016 This thesis for the Doctor of Philosophy degree by Joanne Burnette Cole has been approved for the Human Medical Genetics and Genomics Program by Tasha E. Fingerlin, Chair Richard A. Spritz, Advisor Stephanie A. Santorico Benedikt Hallgrimsson Kristin B. Artinger Date: December 16th, 2016 ii Cole, Joanne Burnette (Ph.D., Human Medical Genetics and Genomics Program) Heritability and Genetic Determinants of Normal Human Facial Shape and Body Size Thesis directed by Professor Richard A. Spritz ABSTRACT Human appearance is a complex assemblage of highly variable anatomic structures that together make each of us unique. Familial similarity, particularly in the face, underscores a genetic component; however, little is known about the genes that underlie differences in physical appearance. We estimated heritability of facial and anthropometric traits in African children and adolescents using genetic relatedness to jointly estimate variance explained by common genetic variation and uncaptured genetic variation, the sum representing narrow- sense heritability. Our facial trait estimates range from 17-67%, with horizontal measures being the most heritable. Facial traits measured in the same physical orientation have high positive genetic correlations, whereas traits in opposite orientations have high negative correlations. Among our anthropometric traits, head circumference and hand length measurements were the most heritable (64.9-98.2%) and were similar to previous European estimates, unlike our estimates for height, weight, and BMI (35.1-48.5%). We carried out GWAS and replication of facial traits in Africans, GWAS of facial traits in Europeans, and GWAS of anthropometric traits in Africans. In Africans, we identified genomewide significant association SNPs in SCHIP1 and PDE8A with facial size and suggestive association of ten additional loci with facial shape. In Europeans, we identified significant association with several different facial traits near the following genes known to be involved in the face: MAFB, PAX9, MIPOL1, ALX3, HDAC3, and PAX1. GWAS of anthropometric traits in Africans identified 49 loci with suggestive association. Candidate genes within these iii loci that have been previously associated in Europeans or demonstrate biologically relevant phenotypes in humans, mice, or cells include RCAN2, ZEB1, SYT1, CCDC91, PDE4D, PDZRN3, and LCT. Using anthropometric data from Africans, we developed normal growth curves and compared these to several references. We identified significant growth faltering that was associated with community-level, academic outcome, and environmental variance of facial shape. We demonstrate the importance of monitoring growth into adolescence using population-specific standards, and show that the environment plays a large role on growth. Overall we present multi-ethnic data on normal variation of facial shape and body size that augment our understanding of physical development and provide insights relevant to human disease and forensics. The form and content of this abstract are approved. I recommend its publication. Approved: Richard A. Spritz iv ACKNOWLEDGEMENTS This work was funded by grants from the National Institutes of Health under the NIDCR FaceBase Initiative (http://www.nidcr.nih.gov/ ; NIDCR DE020054, to R.A.S.), CIDR (http://www.cidr.jhmi.edu/ ; HG006829, to R.A.S.), the National Institute of Justice (http://www.nij.gov/Pages/welcome.aspx ; 2013-DN-BX-K005, to R.A.S.), and the National Science and Engineering Council Discovery Grant (http://www.nserc- crsng.gc.ca/index_eng.asp ; NSERC DG#238992-12, to B.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work was approved by Colorado Multiple Institutional Review Board #09- 0731. See Appendix H for my personal contributions to each chapter. Individuals who have contributed to this work include Mange Manyama, Emmanuel Kimwaga, Joshua Mathayo, Jacinda R. Larson, Denise K. Liberton, Ken Lukowiak, Tracey M. Ferrara, Sheri L. Riccardi, Mao Li, Washington Mio, Michaela Prochazkova, Trevor Williams, Hong Li, Kenneth L. Jones, John R. Shaffer, Ekaterina Orlova, Myoung Keun Lee, Elizabeth J. Leslie, Zachary D. Raffensperger, Carrie L. Heike, Michael L. Cunningham, Jacqueline T. Hecht, Chung How Kau, Nichole L. Nidey. Lina M. Moreno. George L. Wehby, Jeffrey C. Murray, Cecelia A. Laurie, Cathy C. Laurie, Paula N. Gonzalez, Warren M. Wilson, Charles C. Roseman, Jordan J. Bannister, Nils D. Forkert, Eleanor Feingold, Mary L. Marazita. Seth M. Weinberg, Ophir D. Klein, Stephanie A. Santorico, Benedikt Hallgrimsson, and Richard A. Spritz. v TABLE OF CONTENTS CHAPTER I. INTRODUCTION............................................................................................................ 1 II. HERITABILITY AND GENETIC CORRELATIONS OF HUMAN FACIAL SHAPE AND SIZE ........................................................................ 10 III. GENETIC DETERMINANTS OF FACIAL SHAPE I. AFRICANS ................................................................................................................................ 34 IV. GENETIC DETERMINANTS OF FACIAL SHAPE II. USA CAUACASIANS ........................................................................................................ 59 V. NORMATIVE GROWTH CURVES OF AFRICAN CHILDREN AND COMPARISON WITH "INTERNATIONAL" STANDARDS ................................................................................... 81 VI. GROWTH FALTERING, FACIAL SHAPE, AND ENVIRONMENTAL VARIANCE IN TANZANIAN CHILDREN ................................................................................................................................... 109 VII. HERITABILITY OF ANTHROPOMETRIC TRAITS IN AFRICANS ............................................................................................................ 134 VIII. GENETIC DETERMINANTS OF ANTHROPOMETRIC TRAITS IN AFRICANS ............................................................. 148 IX. DISCUSSION ................................................................................................................................ 181 REFERENCES ......................................................................................................................... 196 APPENDIX A. RAPID AUTOMATED LANDMARKING FOR MORPHOMETRIC ANALYSIS OF THREE DIMENSIONAL FACIAL SCANS .......................................................................... 241 B. CHAPTER II SUPPLEMENTAL MATERIAL .................................................... 266 C. CHAPTER III SUPPLEMENTAL MATERIAL ................................................... 275 D. CHAPTER IV SUPPLEMENTAL MATERIAL .................................................. 285 E. CHAPTER V SUPPLEMENTAL MATERIAL .................................................... 322 F. CHAPTER VI SUPPLEMENTAL MATERIAL ................................................... 340 vi G. CHAPTER VIII SUPPLEMENTAL MATERIAL ............................................... 352 H. PERSONAL CONTRIBUTIONS TO EACH CHAPTER ................................. 356 vii LIST OF TABLES CHAPTER II Table 1. Thirty-eight facial phenotypes derived from landmarks on 3D facial scans. Table 2. Heritability of 38 facial traits. CHAPTER III Table 1. Facial size and shape phenotypes tested for genetic association. Table 2. GWAS, replication, and meta-analysis results of replicated association signals. CHAPTER IV Table 1. Genomewide significant meta-analysis results for five traits Table 2. Testing of previously identified genome-wide significant SNPs in European samples. CHAPTER VI Table 1. ANOVA table for analysis of shape correlates of growth, age, and size. Table 2. Multiple linear regression of growth faltering on environmental PCs. CHAPTER VII Table 1. Descriptive Statistics of 8 Anthropometric traits. Table 2. Heritability of 8 Anthropometric traits. CHAPTER VIII Table 1. Suggestive genetic association results with 8 anthropometric traits. Table 2. Direct replication in Africans (P < 0.05) of SNPs previously associated with anthropometric traits in Europeans. Table 3. Replication in Africans of genes previously associated with anthropometric traits in Europeans. viii LIST OF FIGURES CHAPTER II Figure 1. 3D Facial scan with annotated landmarks. Figure 2. Study age distribution by sex. Figure 3. Heritability of 38 facial traits. Figure 4. Heritability of linear distances by measurement orientation. Figure 5. Pairwise genetic correlation matrix of the face. CHAPTER III Figure 1. WHO 2007 Reference BMI Z-scores for the Tanzanian study population. Figure 2. 3D Facial scan with annotated landmarks. Figure 3. SCHIP1 locus associated with centroid size. Figure 4. SCHIP1 locus associated with PC4. Figure 5. PDE8A locus associated with allometry. Figure 6. Expression of Schip1 and Pde8a during mouse embryonic development. CHAPTER IV Figure 1. Set of 20 linear distance measurements used in the current study. Figure 2. LocusZoom plots showing genomewide significant associations observed in the meta-analysis for cranial base width (Figure 1A). Figure 3. LocusZoom plots showing genomewide significant associations observed in the meta-analysis for