Genetic analysis of Bipolar disorder and alcohol use disorder

293 Pages·2015·3.49 MB·English

Genetic Analysis of Bipolar Disorder and
Alcohol Use Disorder

Shareefa Dalvie M.Sc. (Med)
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Thesis Presented for the Dpegree of
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DOCTOR OF PHICLOSOPHY

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in the Division of Human Genetics, Doepartment of Clinical Laboratory Sciences

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UNIVERtSITY OF CAPE TOWN
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i March 2015
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Supervisors: Prof. Raj Ramesar and Prof. Dan J. Stein
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The copyright of this thesis vests in the author. No
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quotation from it or information derived from it is to be

published without full acknowledgeement of the source.
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The thesis is to be used for private study or non-
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commercial research purposes only.

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Published by the Universit y of Cape Town (UCT) in terms
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of the non-exclusive license granted to UCT by the author.
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Plagiarism Declaration

This study was performed from 2011-2015 under the supervision of Prof. Raj Ramesar and
Prof. Dan Stein.
I hereby declare that this thesis is a presentation of my original research work and where
collaborations were involved it has been clearly indicated. It is submitted for the Degree of
Doctor of Philosophy (PhD) in Human Genetics at the University of Cape Town (UCT). I
have used the American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
convention for citation and referencing.

Name: Shareefa Dalvie
Date: 16 March 2015

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Abstract
Background: Mental health disorders represent a major public health problem in most
countries around the world. In South Africa, the lifetime prevalence of psychiatric disorders
is 30.3%, with substance-use disorders and mood disorders being the second and third most
prevalent classes of lifetime disorders, respectively. Bipolar disorder (BD) has a lifetime
prevalence of 1.4% and alcohol use disorder (AUD) a lifetime prevalence of 30.3%, and they
are frequently comorbid. Both of these disorders have a relatively high heritability, yet the
exact genetic basis of each remains unknown. Genetic variants within the hypothalamic-
pituitary-adrenal (HPA)-axis and glutamatergic pathways have previously been implicated in
both phenotypes. The aim of this project was to investigate the aetiology of BD and AUD,
using high-throughput genomic technologies, bioinformatics, brain-imaging and
environmental measures. An additional aim was to assess the genetic aetiology of BD-AUD
comorbidity.
Methods: For the genetic analysis underlying BD, a South African ‗Afrikaner‘ family was
investigated. Whole-genome sequencing (WGS) and whole-genome linkage analysis was
performed for individuals with BD Type I (BDI) and unaffected family members using the
Illumina HiSeq2000 and Affymetrix AxiomTM Genome-wide CEU 1 Array, respectively. For
the AUD analysis, two groups were investigated; a South African adolescent group
comprising 80 individuals with AUD and 80 controls, and a group of 8123 individuals from
the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort. The South
African group of adolescents were genotyped using the Illumina Infinium iSelect custom
6000 BeadChip, childhood trauma data was obtained and brain magnetic resonance images
were collected for a subset of this group. Genotype data on HPA-axis genes were obtained
from a previous study for the ALSPAC cohort. The fourth group of individuals investigated
in this thesis comprised 233 individuals with BD-AUD comorbidity from the Systemic
Treatment Enhancement Program for BD (STEP-BD). Genotype data for genes from the
glutamatergic and HPA-axis pathways were obtained from a previous study conducted on
these individuals.
Results: The chromosomal regions 6p25, 10p14-10p15.1, 11q23-11q25, and 13q21-22
scored the highest LOD scores for BD and the most over-represented pathway in the affected
family members was the T-cell receptor signalling pathway. In the South African adolescent
group, circadian rhythm genes were associated with AUD and childhood trauma predicted
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alcohol use in adolescence. The gene-imaging analysis identified a SNP in the glutamate
receptor, ionotropic, N-methyl D-aspartate 2B (GRIN2B) gene as being associated with brain
volume in the left orbitofrontal cortex and posterior cingulate. HPA-axis genes did not show
an association with AUD and no significant gene x environment interactions were detected
for AUD in the ALSPAC cohort. Single variants in the glutamatergic genes and HPA-axis
were not associated with BD-AUD comorbidity. However, from the gene-based analysis, the
glutamatergic gene PRKCI was associated with BD-AUD comorbidity.
Conclusions: It appears that disruption in immune-related genes may contribute to the
development of BD in an Afrikaner family. No significant gene x environment interactions
were detected for adolescent AUD. The circadian pathway and childhood trauma may play a
role in the development of adolescent AUD. Differential brain volume and BD-AUD
comorbidity may be characterised by variation in the glutamatergic pathway. These pathways
and the interactions between them should be further investigated in BD and AUD.

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Preface
Investigating any single psychiatric disorder is a challenge, as revealed in the literature. In
this exploratory study the candidate investigates two distinct but related (and often co-
morbid) phenotypes (bipolar disorder and alcohol use disorder), using a range of
methodologies. It was hoped that the candidates exposure to these psychiatric phenotypes,
and examination of her own data generated through genomic analyses, and access to data
from other international studies, provide her with skills, and access to resources for future
work in the challenging area of psychiatric genetics/genomics.
This thesis consists of six chapters. Chapter 1 is an introduction, which includes descriptions
and the epidemiology of the two psychiatric phenotypes under investigation, namely bipolar
disorder and alcohol use disorder. Chapter 2 presents the investigation of the genetic basis of
bipolar disorder in an Afrikaner family using whole-genome sequencing and whole-genome
linkage analysis. Chapter 3 includes the investigation on alcohol use disorder in a local
adolescent group using genetic, environmental and brain imaging measures. Brain imaging
and gene-imaging analyses were performed in collaboration with Dr Samantha Brooks from
the Department of Psychiatry and Mental Health at UCT. Chapter 4 provides an investigation
of alcohol use in a European birth cohort, specifically investigating the HPA-axis. Chapter 5
includes the investigation of the glutamate and HPA-axis pathways in a bipolar disorder
group with comorbid alcohol use disorder. Chapter 6 is a concluding chapter for the entire
thesis.

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The Guest House

This being human is a guest house.
Every morning a new arrival.

A joy, a depression, a meanness,
some momentary awareness comes
as an unexpected visitor.

Welcome and entertain them all!
Even if they're a crowd of sorrows,
who violently sweep your house
empty of its furniture,
still, treat each guest honorably.
He may be clearing you out
for some new delight.

The dark thought, the shame, the malice,
meet them at the door laughing,
and invite them in.

Be grateful for whoever comes,
because each has been sent
as a guide from beyond.

-Rumi

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Acknowledgements

Thank you to my Creator, for guiding me through this challenging task.
The completion of this thesis would not have been possible without the contribution of the following
individuals:
My supervisors, Prof. Raj Ramesar and Prof. Dan Stein, your mentorship, advice and support have been
invaluable. I am very grateful to have had a place on this complex project.
Thank you to all the participants of this study. Without you this research would not have been possible.
Mr Gerrit Botha from CBIO for doing the whole genome sequence analysis.
Dr Morne du Plessis for your immense help with the bioinformatics analysis.
Prof. James Knowles for allowing me the opportunity to visit your lab and generate the whole genome
sequences.
The CPGR and Jo McBride for running the Affymetrix array.
Dr Samantha Brooks for assistance with the brain imaging and gene-imaging aspect of the AUD study.
Prof. David Baldwin and EUSARNAD for providing me with the opportunity to visit the University of Bristol.
Prof. Glyn Lewis, Dr Sarah Lewis and Mr Andrew Crawford, Assoc. Prof Fazil Aliev and Prof. Danielle Dick
for your assistance with the analysis of the ALSPAC dataset.
Dr Chiara Fabbri and Prof. Alessandro Seretti for your help and guidance with the analysis of the STEP-BD
dataset.
Prof Karestan Koenen for the funding of the Illumina microarray and advice on statistical analysis.
Sr Gameda Benefeld for your unfailing support.
Assoc/Prof Collet Dandara for your advice and mentorship.
Lindiwe Lamola, Tasneem Salie, Horacia Naidoo, Maryam-Bibi Rumaney, and Amy Roberts for all the laughs
and support.
The Division of Human Genetics for having me as part of the family for the past 7years.
I would also like to thank my funders, the University of Cape Town and NRF-DAAD.
Lastly, and most importantly, thank you to my parents, my siblings, nieces and nephews for your unwavering
support, patience and encouragement.
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Table of Contents
Plagiarism Declaration ............................................................................................................... ii
Abstract .................................................................................................................................... iii
Preface........................................................................................................................................ v
The Guest House ....................................................................................................................... vi
Acknowledgements .................................................................................................................. vii
List of Figures ........................................................................................................................ xiii
List of Tables .......................................................................................................................... xiv
Abbreviations ........................................................................................................................... xv
Chapter 1: Introduction .............................................................................................................. 1
Background ............................................................................................................................ 1
1.1 Epidemiology of Psychiatric Disorders: Worldwide and in South Africa .................. 1
1.2 Classes of Psychiatric Diagnoses ................................................................................ 2
1.3 Mood Disorders ........................................................................................................... 3
1.3.1 Bipolar Disorder– A Historical Perspective ............................................................. 3
1.3.2 Diagnostic Classification of BDI .............................................................................. 4
1.4 Substance-Related Disorders....................................................................................... 5
1.5 Overlap of Psychiatric Diagnoses ............................................................................... 9
1.5.1 Overlap in BD and AUD......................................................................................... 10
1.6 Project Aims and Objectives .......................................................................................... 11
1.6.1 Objectives ............................................................................................................... 11
Chapter 2: An Investigation of the Genetics Underlying Bipolar Disorder ............................. 12
Abstract ................................................................................................................................ 12
2.1 Introduction .................................................................................................................... 12
2.1.1 Genetic Basis of BD................................................................................................ 12
2.1.2 Next Generation Sequencing Technologies and Complex Disorders ..................... 24
2.1.3 Aims and Objectives ............................................................................................... 26
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2.2 Materials and Methods ................................................................................................... 27
2.2.1 Research Group ....................................................................................................... 27
2.2.2 Genetic Analysis ..................................................................................................... 28
2.2.3 Statistical and Bioinformatic Analyses ................................................................... 31
2.3 Results ............................................................................................................................ 36
2.3.1 Research Group ....................................................................................................... 36
2.3.2 Statistical and Bioinformatic Analyses ................................................................... 37
2.4 Discussion ...................................................................................................................... 47
Chapter 3: An Investigation of AUD in a Group of South African Adolescents .................... 52
Abstract ................................................................................................................................ 52
3.1 Introduction .................................................................................................................... 52
3.1.1 Addiction and the Neurobiology Underlying Alcohol Use .................................... 53
3.1.2 Aims and Objectives ............................................................................................... 66
3.2 Materials and Methods ................................................................................................... 69
3.2.1 Research Group ....................................................................................................... 69
3.2.2 Clinical Measures.................................................................................................... 70
3.2.3 Genetic Analysis ..................................................................................................... 71
3.2.4 Imaging Analysis .................................................................................................... 72
3.2.5 Statistical Analysis .................................................................................................. 73
3.3 Results ............................................................................................................................ 77
3.3.1 Research Group ....................................................................................................... 77
3.3.2 Clinical Measures.................................................................................................... 77
3.3.3 Statistical Analysis .................................................................................................. 78
3.4 Discussion ...................................................................................................................... 87
Chapter 4: An Investigation of Alcohol Use in a Group of Adolescents from the ALSPAC
Cohort ...................................................................................................................................... 91
Abstract ................................................................................................................................ 91
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