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Association Analyses of Known Genetic Variants with Gene

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Association Analyses of Known Genetic Variants with Gene ASSOCIATION ANALYSES OF KNOWN GENETIC VARIANTS WITH GENE EXPRESSION IN BRAIN by Viktoriya Strumba A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2009 Doctoral Committee: Professor Margit Burmeister, Chair Professor Huda Akil Professor Brian D. Athey Assistant Professor Zhaohui S. Qin Research Statistician Thomas Blackwell To Sam and Valentina Dmitriy and Elizabeth ii ACKNOWLEDGEMENTS I would like to thank my advisor Professor Margit Burmeister, who tirelessly guided me though seemingly impassable corridors of graduate work. Throughout my thesis writing period she provided sound advice, encouragement and inspiration. Leading by example, her enthusiasm and dedication have been instrumental in my path to becoming a better scientist. I also would like to thank my co-advisor Tom Blackwell. His careful prodding always kept me on my toes and looking for answers, which taught me the depth of careful statistical analysis. His diligence and dedication have been irreplaceable in most difficult of projects. I also would like to thank my other committee members: Huda Akil, Brian Athey and Steve Qin as well as David States. You did not make it easy for me, but I thank you for believing and not giving up. Huda’s eloquence in every subject matter she explained have been particularly inspiring, while both Huda’s and Brian’s valuable advice made the completion of this dissertation possible. I would also like to thank all the members of the Burmeister lab, both past and present: Sandra Villafuerte, Kristine Ito, Cindy Schoen, Karen Majczenko, Ellen Schmidt, Randi Burns, Gang Su, Nan Xiang and Ana Progovac. You all taught me something new, gave iii me a little bit of yourself. Separate thank you to Elżbieta Śliwerska for patiently teaching me lab techniques and for being a good friend. A special thank you goes to my parents Dr.Reznik and Dr.Vyunitskaya. You have been my inspiration throughout my life. I wish you lots of health and hope I can continue to learn from you for many years to come. A very special thank you goes to my husband who pushed and pulled, held on and pressed forward, stood by my side and stood out of my way. I could not do it without you! I also would like to thank my immediate and extended family: Eugenia, Alesha, Dina, Larisa, Raisa Il’inichna, Mikhail Markovich, Grigoriy Davidovich, Lyubov Ivanovna, Anna, Zhenya, Vera, Yasha and Phillip. Of course it would not be possible without Ilya Wagner, who has been the best uncle my precious daughter Elizabeth could ask for! iv TABLE OF CONTENTS DEDICATION ............................................................................................................................. ii ACKNOLEDGEMENTS.......................................................................................................... iii LIST OF TABLES ..................................................................................................................... vii LIST OF FIGURES .................................................................................................................. viii CHAPTER I INTRODUCTION..................................................................................................1 DNA microarrays technology is a platform for quantifying molecular phenotypes ...................................................................................................2 Expression studies of Mendelian disorders .................................................5 Association studies of complex disorders ...................................................8 References ..................................................................................................13 II GLUTAMATE SIGNALLING IMPLICATED IN CAYMAN ATAXIA BY MICROARRAY ANALYSIS OF ITS MOUSE MODEL ...............................17 Introduction ................................................................................................17 Materials and Methods ..............................................................................20 Results .......................................................................................................23 Discussion ..................................................................................................28 Figures........................................................................................................34 Tables .........................................................................................................36 References ..................................................................................................46 v III EXPRESSION PROFILING IMPLICATES DYSREGULATION OF CALCIUM SIGNALING IN WADDLES (WDS), A MOUSE MODEL OF ATAXIA AND DYSTONIA ............................................................. 51 Introduction ................................................................................................51 Materials and Methods ..............................................................................53 Results .......................................................................................................54 Discussion ..................................................................................................56 Tables .........................................................................................................62 References ..................................................................................................70 IV ANALYSIS OF GENE EXPRESSION ASSOCIATION WITH BIPOLAR DISORDER ASSOCIATED SNPS ....................................................................73 Introduction ................................................................................................73 Materials and Methods ..............................................................................80 Results .......................................................................................................82 Discussion ..................................................................................................87 Figures........................................................................................................89 Tables .........................................................................................................95 References ..................................................................................................96 V DISCUSSION ......................................................................................................99 Figures......................................................................................................118 References ................................................................................................119 vi LIST OF TABLES CHAPTER II 2.1 Genes consistently differentially expressed in whole brain and cerebellum experiments ....................................................................................................36 2.2 qRT-PCR primer pairs ....................................................................................44 2.3 Results of qRT-PCR .......................................................................................45 CHAPTER III 3.1 Subset of genes differentially expressed in cerebellum of waddles mice compared to controls ......................................................................................62 CHAPTER IV 4.1 Summary of the data used for the regression analysis of gene expression against SNPs ...................................................................................................95 vii LIST OF FIGURES CHAPTER II 2.1 Differentially expressed genes in Atcay mutants compared to control cerebellum ......................................................................................................34 2.2 Mouse models of ataxia ..................................................................................35 CHAPTER IV 4.1 Significant association between SNPs and transcripts in cis seen in all 6 brain regions tested ..................................................................................................89 4.2 Top cis associations are due to SNPs in LD with each other in regions on chromosomes 3 and5 ......................................................................................90 4.3 Expression levels of MCTP1 gene are associated with variants of rs212448 SNP consistently across brain regions ............................................................91 4.4 Bipolar GWAS association p-values peak does not overlap with SNP- expression p-values peak ................................................................................92 4.5 Association between MCTP1 and rs211448 is replicated in all disorders samples in this study .......................................................................................93 4.6 Plot of –log10 p-values for BP GWA study meta-analysis for region on chromosome 3 ................................................................................................94 CHAPTER V 5.1 Basic circuitry of the cerebellar cortex .........................................................118 viii CHAPTER I INTRODUCTION It has long been accepted that genetic variations underlie phenotypic differences between individuals of the same species. There are many different types of DNA variations, including single nucleotide polymorphisms (SNPs), as well as inversions, insertions and deletions (the latter can range from one or a few bases to parts of chromosomes).
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