Searching for susceptibility genes for psychosis in late-onset Alzheimer's disease

476 Pages·2013·16.68 MB·English

Searching for susceptibility genes for
psychosis in late-onset Alzheimer’s
disease
Rebecca Sims
Department of Psychological Medicine,
School of Medicine, Cardiff University.
Supervisors;
Professor Julie Williams
Dr. Richard Abraham
UMI Number: U584408
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Contents
List of Figures
List of Tables
Acknowledgements
General Abstract
1. General Introduction: Psychosis in Alzheimer’s disease
1.1. Alzheimer’s disease
1.1.1. Genetics of Alzheimer's disease
1.1.2. Neuropathology and Neurochemistry of
Alzheimer’s disease
1.1.3. Environmental Risk Factors for Alzheimer’s disease
1.2. Psychosis in Alzheimer’s disease
1.2.1. Development of Psychosis in Alzheimer’s disease
1.2.2. Classification of Alzheimer’s disease with Psychosis
1.3. Environmental Risk Factors for Alzheimer’s disease with
Psychosis
1.4. Mapping Complex Traits
1.4.1. Familiality
1.4.2. Heritability
1.4.3. Linkage Analysis
1.4.4. Association Analysis
1.4.5. Replication of Association Studies
1.4.6. Linkage Disequilibrium
1.5. Genetics of Alzheimer’s disease with Psychosis
1.5.1. Familiality of Alzheimer’s disease with Psychosis
1.5.2. Heritability of Alzheimer’s disease with Psychosis
1.5.3. Linkage Analyses of Alzheimer’s disease with Psychosis
1.5.4. Association Analyses of Alzheimer’s disease with
Psychosis
1.6. Study Design
1.7. General Aims
1.8. Thesis Outline
2. Materials and Methods
2.1. Sample Ascertainment 47
2.1.1. MRC Genetic Resource for LOAD Sample 47
2.2. Behavioural Assessment 48
2.2.1. The Neuropsychiatric Inventory 48
2.2.2. Principle Components Analysis 49
2.2.3. Sample Classification Criteria 49
2.3. Marker Selection 50
2.4. DNA Extraction, Quantification, Storage and Sample Preparation 51
2.4.1. DNA Extraction 51
2.4.2. DNA Quantification 51
2.4.3. Liquid Handling 52
2.4.4. DNA Storage 52
2.4.5. Sample Preparation 53
2.5. Polymerase Chain Reaction 53
2.5.1. Oligonucleotide Primer Design 55
2.5.2. PCR Reagents 55
2.5.3. PCR Condition Optimisation 56
2.6. Agarose Gel Electrophoresis 57
2.7. Genotyping Methods 59
2.7.1. Genescan Fluorescent PCR 59
2.7.2. Amplifluor™ UniPrimer Chemistry 61
2.7.3. Sequenom™ iPlexGOLD™ MassARRAY™ 65
2.7.3.1. Multiplex Assay Design 65
2.7.3.2. Multiplex Assay PCR 66
2.7 3.3. PCR Purification 67
2.7.3 4. iPlexGOLD™ Primer Extension 67
2.7.3.5. Extension Product Desalting 69
2.7.3.6. Running and Analysing Spectra 69
2.7.4. Quality Control 71
2.8. Data Storage 71
2.9. Statistical Analysis 72
2.9.1. PUNK 72
2.9.2. HAPLOVIEW 73
2.9.3. UNPHASED 74
//
2.9.4. R 75
2.9.5. WGAViewer 75
2.9.6. Power calculations 76
2.10. Bioinformatics 78
2.10.1. National Center for Biotechnology Information 78
2.10.2. University of California Santa Cruz Genome Browser 79
2.10.3. The International HapMap Project 80
2.10.4. Ensembl Genome Browser 81
2.10.5. Schizophrenia Gene 81
2.10.6. SNP Annotation and Proxy Search 82
2.11. Conservation and Transcription Factor Binding Site Prediction 82
2.11.1. Cluster Buster 82
2.11.2. University of California Santa Cruz Most
Conserved Track 83
2.11.3. Evolutionary Conserved Region Browser 84
3. Psychosis Candidate Gene Association Study 86
3.1. Introduction 86
3.2. Genotyping Strategy 87
3.3. Disrupted in Schizophrenia 1 92
3.3.1. Literature Summary 96
3.3.2. Study Design 96
3.3.3. Results 97
3.3.4. Discussion 98
3.4. Dystrobrevin Binding Protein 1 101
3.4.1. Literature Summary 103
3.4.2. Study Design 105
3.4.3. Results 105
3.4.4. Discussion 108
3.5. Glutamate Receptor lonotropic Kainate 2 108
3.5.1. Literature Summary 110
3.5.2. Study Design 110
3.5.3. Results 112
3.5.4. Discussion 112
3.6. Glutamate Receptor Metabotropic 3 116
in
3.6.1. Literature Summary 118
3.6.2. Study Design 119
3.6.3. Results 121
3.6.4. Discussion 122
3.7. Neuregulin 1 125
3.7.1. Literature Summary 127
3.7.2. Study Design 129
3.7.3. Resu/fs 129
3.7.4. Discussion 135
3.8. Brain-derived Neurotrophic Factor 135
3.8.1. Literature Summary 139
3.8.2. Study Design 139
3.8.3. Results 140
3.8.4. Discussion 143
3.9. D-amino Acid Oxidase Activator 143
3.9.1. Literature Summary 146
3.9.2. Study Design 146
3.9.3. Results 149
3.9.4. Discussion 149
3.10. 2\3’-Cyclic Nucleotide 3’ Phosphodiesterase 152
3.10.1. Literature Summary 154
3.10.2. Study Design 156
3.10.3. Results 156
3.10.4. Discussion 159
3.11. Oligodendrocyte Lineage Transcription Factor 2 159
3.11.1. Literature Summary 162
3.11.2. Study Design 163
3.11.3. Results 163
3.11.4. Further Work 171
3.11.5. Discussion 176
3.12. Catechol-O-Methyl Transferase 177
3.12.1. Literature Summary 180
3.12.2. Study Design 180
3.12.3. Results 181
zv
3.12.4. Discussion 181
3.13. Discussion 184
4. Replication of Schizophrenia GWAS 187
4.1. Introduction 187
4.2. Study Design 190
4.3. Genotyping Strategy 191
4.4. Results 193
4.4.1. Comparison with O’Donovan GWAS 202
4.5. Discussion 203
5. Genome-Wide Association Study of LOAD with Psychosis 207
5.1. Introduction 207
Section 1: LOAD+P GWAS 210
5.2. Materials and Methods 210
5.2.1. Sample Ascertainment and Diagnostic Criteria 210
5.2.2. Sample Sets 211
5.2.3. DNA Extraction, Sample Preparation and
Laboratory Quality Control 211
5.2.4. Genotyping 212
5.2.5. Individual Quality Control 212
5.2.6. SNP Quality Control 214
5.2.7. Study Power 215
5.2.8. Association Analyses 220
5.3. Results 222
Section 2: Secondary Analyses 234
5.4. Introduction 234
5.5. Materials and Methods 235
5.6. Results 235
5.6.1. SNP Based Analyses 235
5.6.2. Gene Based Analyses 241
5.7. Discussion 252
6. Final Discussion 257
6.1. Thesis Findings 258
6.2. Thesis Limitations 262
6.3. Future Work 264
v
6.4. Conclusions 267
Appendices 269
Chapter 3 Appendix 270
Chapter 4 Appendix 306
Chapter 5 Appendix 311
Abbreviations 393
Bibliography 399
vi
List of Figures
Chromosome 2. Multipoint MLS for families with LOAD+P
and LOAD+P with APOE e4 allele. 26
Chromosome 6. Multipoint MLS for families with LOAD+P
and LOAD+P with APOE e4 allele. 27
Chromosome 21. Multipoint MLS for families with LOAD+P
and LOAD+P with APOE z4 allele. 28
Covariant linkage analysis of LOAD-P and LOAD-P+e4
on chromosome 7q. 31
Covariant linkage Analysis of LOAD-P and LOAD-P+e4
on chromosome 15q. 32
Covariant linkage Analysis of LOAD+P and LOAD+P+e4 on
chromosome 6q. 33
Covariant linkage Analysis of LOAD+P and LOAD+P+e4 on
chromosome 21. 34
Schematic of DNA amplification by Polymerase Chain reaction. 54
Schematic of the step-by-step Amplifluor™ reaction. 62
Schematic of the Sequenom™ iPlex™ Assay. 70
The DISC1 locus. 95
The DTNBP1 locus. 104
The GRIK2 locus. 111
The GRM3 locus. 120
The NRG1 locus. 128
The BDNF locus. 138
The DAOA locus. 148
The CNP locus. 155
The OLIG2 locus. 161
Representation of ECR browser output for OLIG2 region. 168
Output from UCSC most conserved track for the OLIG2 gene. 169
Output from Cluster Buster software for the OLIG2 gene. 170
The OLIG1 locus. 173
The COMT locus. 179
vii