Copy Number Variation in Neuropsychiatric Disorders
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UNIVERSITY OF CALIFORNIA Los Angeles Copy Number Variation in Neuropsychiatric Disorders A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics by Alden Yen-Wen Huang 2018 © Copyright by Alden Yen-Wen Huang 2018 ABSTRACT OF THE DISSERTATION Copy Number Variation in Neuropsychiatric Disorders by Alden Yen-Wen Huang Doctor of Philosophy in Bioinformatics University of California, Los Angeles, 2018 Professor Giovanni Coppola, Chair In this thesis, I characterize the contribution of rare copy number variation (CNV) to the genetic etiology of Tourette syndrome (TS) and bipolar disorder (BP). I accomplish this using several different study designs and various methods for CNV detection. As array data was widely available for the majority of samples evaluated, I make extensive use of this technology throughout this project and first provide an overview of the technical challenges involved and describe the analytical pipeline I developed to produce reliable CNV calls from such data. Then, in the largest TS CNV study conducted to date, I report the discovery of the first two genome-wide significant CNVs associated with the disorder, and demonstrate an increased global burden of large, singleton events and CNVs at known, pathogenic loci. Conditioned on this latter observation, I perform an exploratory analysis aimed at gene discovery through the identification of de novo copy number variants from whole-exome sequencing in a sample of affected proband, unaffected parent trios in TS. ii I then describe a CNV study of 26 large, multigenerational families with a high incidence of BP from two population isolates, using both microarray and whole-genome sequencing data. While thorough examination of these extended BP pedigrees revealed no segregating variants of large effect, I observe a significant increase in CNV burden across a subset of BP-related genes. Finally, I explore this notion further in a larger North American sample of unrelated individuals ascertained for BP. I demonstrate that although BP cases show no observable differences in the rate or size of rare CNVs, case CNVs affect more highly constrained, brain- expressed genes, and I provide evidence for an increased female CNV burden for BP. iii The dissertation of Alden Yen-Wen Huang is approved. Jeremiah Scharf Bogdan Pasaniuc Nelson B. Freimer Eleazar Eskin Giovanni Coppola, Committee Chair University of California, Los Angeles 2018 iv To my family. v Table of Contents Chapter 1: Introduction ............................................................................................................1 1.1 The landscape of human genetic variation ...................................................................2 1.2 Overview of methods for genome-wide detection of copy number variation ..................3 1.3 Copy number variation and human disease ..................................................................6 1.4 Rationale ......................................................................................................................8 Chapter 2: A Workflow for Robust Detection of CNVs Using SNP Arrays ............................9 2.1 Abstract ......................................................................................................................10 2.2 Background ................................................................................................................11 2.3 Overview of the CNV calling pipeline ..........................................................................12 2.4 A computational framework for the analysis of large-scale CNV studies .....................20 Chapter 3: Rare Copy Number Variation Increases Risk for Tourette Syndrome ..............22 3.1 Abstract ......................................................................................................................23 3.2 Background ................................................................................................................24 3.3 Sample collection and genome-wide detection of rare CNVs ......................................27 3.4 Global burden analysis of rare CNVs in TS ................................................................28 3.5 Enrichment of large, singleton events and CNVs affecting conserved genes ..............31 3.6 Enrichment of known pathogenic neurodevelopmental CNVs .....................................33 3.7 Deletions in NRXN1 and duplications in CNTN6 confer substantial risk for TS ...........33 3.8 Phenotypic characteristics of NRXN1 and CNTN6 CNV carriers ................................36 3.9 Spatio-temporal brain expression patterns of NRXN1 and CNTN6 .............................37 3.10 Discussion ................................................................................................................38 3.11 Methods ...................................................................................................................44 Chapter 4: Identification of De Novo CNVs in Sporadic TS Trios Using WES ....................57 4.1 Abstract ......................................................................................................................58 4.2 Background ................................................................................................................59 4.3 Sample sequencing and CNV calling ..........................................................................60 4.4 Identification and validation of de novo events............................................................61 vi 4.5 Discussion ..................................................................................................................63 4.6 Methods .....................................................................................................................67 Chapter 5: Contribution of Common and Rare Variation to BP Susceptibility in Extended Pedigrees from Population Isolates.......................................................................................70 5.1 Abstract ......................................................................................................................71 5.2 Background ................................................................................................................72 5.3 Genotyping and sequencing of CO/CR BP1 families ..................................................73 5.4 Characteristics of admixture in the CO/CR Extended Pedigrees ................................76 5.5 The effect of common variation on BP1 in CO/CR pedigrees .....................................76 5.6 The effect of rare variation on BP1 in CO/CR pedigrees .............................................78 5.7 Genetic Loci Segregating with BP1 in the CO/CR Extended Pedigrees ......................82 5.8 Discussion ..................................................................................................................87 5.9 Methods .....................................................................................................................90 Chapter 6: Specific Enrichment of Genic Rare CNV Burden in Bipolar Disorder ............. 105 6.1 Abstract .................................................................................................................... 106 6.2 Background .............................................................................................................. 107 6.3 Sample collection, QC, and CNV calling ................................................................... 109 6.4 Burden analysis: CNV event type and size ............................................................... 112 6.5 Burden analysis: genic content ................................................................................. 112 6.6 Evidence for increased female CNV burden in BP .................................................... 116 6.7 Discussion ................................................................................................................ 117 6.8 Methods ................................................................................................................... 120 Appendix A: Supplementary Material for Chapter 3 ........................................................... 124 Appendix B: Supplementary Material for Chapter 5 ........................................................... 136 Appendix C: Supplementary Material for Chapter 6 ........................................................... 140 References ............................................................................................................................ 144 vii List of Figures and Tables Figure 1-1. Methods for CNV detection. ......................................................................................5 Figure 2-1. Parameters used for CNV detection from SNP arrays. ............................................12 Figure 2-2. Schematic overview of the CNV processing pipeline. ..............................................14 Figure 2-3. Effect of custom cluster definition on downstream CNV calling. ..............................15 Figure 2-4. Quality control measures for CNV calling. ...............................................................17 Figure 2-5. A framework for data handling, QC, and rapid visualization for large CNV studies. .21 Figure 3-1. Rare CNV burden in 2,434 TS cases and 4,093 controls. .......................................30 Figure 3-2. Large, singleton CNVs and known pathogenic variants are overrepresented in TS. 32 Figure 3-3. Significant