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Methods and Genome-Wide Association Study for Meiotic Nondisjunction of Chromosome 21

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Methods and Genome-Wide Association Study for Meiotic Nondisjunction of Chromosome 21 Title Page Methods and Genome-Wide Association Study for Meiotic Nondisjunction of Chromosome 21 by Jonathan McKelvey Chernus BS, BA, University of Pittsburgh, 2010 MA, University of Pittsburgh, 2012 Submitted to the Graduate Faculty of the Graduate School of Public Health in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2021 Committee Membership Page UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH This dissertation was presented by Jonathan McKelvey Chernus It was defended on July 27, 2021 and approved by Dissertation Advisor: Eleanor Feingold, PhD Professor Departments of Biostatistics and Human Genetics Graduate School of Public Health University of Pittsburgh Committee Members: Candace M. Kammerer, PhD Associate Professor Department of Human Genetics Graduate School of Public Health University of Pittsburgh John R. Shaffer, PhD Assistant Professor Departments of Human Genetics and Oral and Craniofacial Sciences Graduate School of Public Health and School of Dental Medicine University of Pittsburgh George C. Tseng, ScD Professor Departments of Biostatistics, Human Genetics, and Computational & Systems Biology Graduate School of Public Health University of Pittsburgh ii Copyright © by Jonathan McKelvey Chernus 2021 iii Abstract Methods and Genome-Wide Association Study for Meiotic Nondisjunction of Chromosome 21 Jonathan McKelvey Chernus, PhD University of Pittsburgh, 2021 ABSTRACT Up to one quarter of human conceptions may be aneuploid, having too many or too few chromosomes relative to the standard 23 pairs. Most often this results from nondisjunction in maternal meiosis, making such errors a leading cause of pregnancy loss and congenital abnormalities. Prior research has established advanced age and altered patterns of meiotic recombination as risk factors for maternal meiotic nondisjunction and has shown that meiosis I and II errors may involve different mechanisms, but genetic risk factors have not been systematically investigated. The goal of this dissertation is to advance our knowledge of aneuploidy by identifying and characterizing common genetic variants associated with maternal meiotic nondisjunction of chromosome 21, the most common aneuploid condition in conceptions that survive to term. The first aim was to perform a candidate gene and genome-wide association study (GWAS) in which cases are mothers who have had a child with Down syndrome and controls are the fathers. We found plausible associations at variants at relevant loci. Stratifying by the stage of meiosis in which nondisjunction occurred (MI or MII), our results are consistent with general nondisjunction risk factors as well as some that could be specific for MI or MII. In the second aim, we called recombination events on chromosome 21 in our data set in order to classify cases (mothers) according to their recombination profiles. We therefore developed and implemented novel methods for calling recombination events in both trios and dyads, finding iv that full-data trios can be used to successfully train the method for calling recombination in dyads, which contain less information. The third aim was to further characterize the candidate gene and GWAS associations by performing stratified analyses in subgroups of mothers defined by recombination profile and maternal age. We interpret the associations in the context of possible meiotic error mechanisms. The public health significance of this research is its improvement of our understanding of the genetic architecture of meiotic errors, a leading factor in pregnancy loss and congenital defects. Eventually this could lead to identifying those at higher risk of meiotic errors and enabling more informed reproductive choices. v Table of Contents 1.0 INTRODUCTION................................................................................................................... 1 1.1 BACKGROUND AND MOTIVATION ....................................................................... 1 1.1.1 Meiosis, Aneuploidy, and Established Risk Factors .........................................1 1.1.2 Possible Mechanisms and Genes of Interest ......................................................2 1.2 GENOTYPING ARRAY DATA IN THE CONTEXT OF DOWN SYNDROME... 4 1.2.1 Family Data and Informative Markers ..............................................................4 1.2.1.1 Methods for Trios .................................................................................... 5 1.2.1.2 Methods for Dyads ................................................................................... 9 1.2.2 Description of Data Set ......................................................................................12 1.3 AIMS AND SUMMARY OF THIS DISSERTATION ............................................. 13 1.3.1 Finding Genetic Risk Factors for Nondisjunction ..........................................13 1.3.2 Using Family Data to Call Recombination Events on Chromosome 21 ........14 1.3.3 Characterizing Genetic Risk Factors for Nondisjunction ..............................14 2.0 A CANDIDATE GENE ANALYSIS AND GWAS FOR GENES ASSOCIATED WITH MATERNAL NONDISJUNCTION OF CHROMOSOME 21 ............................. 15 2.1 CHAPTER OVERVIEW ............................................................................................. 16 2.2 AUTHOR SUMMARY ................................................................................................ 16 2.3 INTRODUCTION ........................................................................................................ 17 2.4 METHODS .................................................................................................................... 22 2.4.1 Study Sample ......................................................................................................22 2.4.1.1 Ethics Statement .................................................................................... 22 vi 2.4.1.2 Genotyping ............................................................................................. 23 2.4.1.3 Adjustment for Population Structure .................................................. 25 2.4.1.4 Imputation .............................................................................................. 25 2.4.1.5 Phenotyping ............................................................................................ 25 2.4.2 Analysis ...............................................................................................................27 2.4.2.1 Sample Size ............................................................................................. 27 2.4.2.2 Association Studies ................................................................................ 27 2.4.2.3 Maternal Age Effect............................................................................... 29 2.4.2.4 Candidate Gene Analyses ...................................................................... 30 2.4.2.5 Follow-up Analyses to Examine Top-Ranked GWAS Signals........... 30 2.5 RESULTS ...................................................................................................................... 30 2.5.1 Candidate Gene Association Studies ................................................................30 2.5.1.1 Candidate Genes Associated with Chromosome Segregation ........... 32 2.5.1.2 Genes Association with Human Genome-Wide Recombination Counts (Shown in the Bottom Half of Table 2.2, Below the Double Line) ................ 40 2.5.2 Strongest Results from the Genome-Wide Association Study .......................43 2.5.2.1 rs10948101 on chromosome 6 near VEGFA ........................................ 47 2.5.2.2 rs11535058 on chromosome 2 near SLC39A10 ................................... 49 2.5.2.3 rs35288347 on chromosome 19 near AURKC ...................................... 51 2.5.2.4 rs9984132 on chromosome 21 located in a gene rich region .............. 53 2.5.2.5 rs73178888 on chromosome 8 near a region associated with meiotic recombination .................................................................................................... 55 2.5.2.6 rs115281615 on chromosome 4 near CPEB2 ....................................... 57 vii 2.5.2.7 rs2560850 on chromosome 5 in an intron of MYO10.......................... 59 2.5.3 Strongest Results from the TDT Analyses .......................................................61 2.6 DISCUSSION ................................................................................................................ 62 2.6.1 Genes Associated with Cohesin Complex ........................................................62 2.6.2 Genes Associated with the Synaptonemal Complex (SC)...............................63 2.6.3 Association with Recombination-Related Variants ........................................64 2.6.4 Gene Discovery ...................................................................................................66 2.6.5 Conclusion and Future Directions ....................................................................66 2.7 ACKNOWLEDGMENTS ............................................................................................ 67 3.0 ANALYSES STRATIFIED BY MATERNAL AGE AND RECOMBINATION FURTHER CHARACTERIZE GENES ASSOCIATED WITH MATERNAL NONDISJUNCTION OF CHROMOSOME 21 .................................................................. 68 3.1 CHAPTER OVERVIEW ............................................................................................. 68 3.2 INTRODUCTION .......................................................................................................
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