Ankylosing spondylitis (AS) is an inflammatory arthritis that primarily affects the spine and sacroiliac joints in the pelvis. It is relatively common, affecting 0.4 – 1.4% of white Europeans. It is a complex genetic disease with high heritability, and with environmental factors playing only a minor role. HLA-B*27 is present in 80 - 90% of AS patients and is one of the strongest associations between a major histocompatibility allele and disease known.
Anterior uveitis (AU) occurs commonly in ankylosing spondylitis and is inflammation of the anterior part of the uveal tract encompassing the iris and pars ciliaris of the ciliary body. Infectious agents can cause AU but in European populations immune-mediated processes cause nearly all cases. It is a common complication of AS, but also occurs in isolation. Immune-mediated AU typically has a sudden unilateral onset and limited duration, and this is termed acute anterior uveitis. Acute anterior uveitis is also strongly associated with HLA-B*27.
This thesis examines the genetics of AS and acute anterior uveitis using array based genotyping and statistical genetic techniques to:
(1) Investigate the complex chromosome 5q15 locus that has previously been associated with AS, using data from the Illumina Immunochip genotyping platform,
(2) Investigate the genetic associations of acute anterior uveitis, using the data from Illumina Immunochip genotyping platform,
(3) Investigate the genetic associations of acute anterior uveitis using the Illumina Human Exomechip platform, and
(4) Investigate the genetic associations of AS using data from the Illumina Human Exomechip platform.
Participants were recruited from rheumatology clinics and ophthalmology departments from Australia, the United Kingdom, the United States and New Zealand. Anterior uveitis samples were recruited from rheumatology clinics and ophthalmology clinics in Australia, the United Kingdom, the United States and New Zealand.
The first chapter reviews of the clinical features, epidemiology, immunology and genetics of AS and acute anterior uveitis. It identifies the major associations reported to date and in AS the different ethnic genetic associations described. It discusses how this has contributed to our understanding of disease mechanisms in AS and acute anterior uveitis.
The second chapter describes the detailed analysis of the chromosome 5q15 locus in the AS Immunochip based experiment. This analysis utilized 9,074 cases and 13,607 controls of European descent and 1,550 cases and 1,567 controls of east Asian descent. The locus was examined for association using logistic regression, linear mixed models and Bayesian analysis methods. Association in the genes ERAP2/LNPEP that is seen in HLA-B*27 negative subjects, or on conditioning on the major risk alleles in ERAP1, is described.
The third chapter details the Immunochip analysis of acute anterior uveitis in 289 cases with acute anterior uveitis alone, 1,422 cases with AS and acute anterior uveitis, and 2,339 cases with AS and without acute anterior uveitis. Novel associations are identified using genotyped and imputed data.
The fourth chapter describes the Exomechip analysis of AS in 4,599 cases and 23,554 healthy controls. This study found novel associations that were genome wide signifciant in USP8, C1orf106, and CDKAL1, Novel suggestive associations were found in FAM118A, C7orf72, FAM114A1 and PNPLA1. The associations with C1orf106, CDKAL1 and C7orf72 are associated with inflammatory bowel disease. There was also a secondary signal in the TLR10 gene after conditioning on the association evident in FAM114A1.
The fifth chapter describes a study using Exomechip data to investigate the genetic associations of acute anterior uveitis. This experiment used 2 designs, firstly AS patients with acute anterior uveitis were compared to AS patients without acute anterior uveitis. Secondly AS patients with acute anterior uveitis were compared to healthy controls and AS patients without acute anterior uveitis were compared to healthy controls. A heterogeneity test was then applied to determine if the effect size of associations were different between these two groups. This study confirmed previous findings that HLA-B*27 is an risk factor for acute anterior uveitis in addition to AS disease status. SNPs in ERAP1 (rs30187) and ERAP2 (rs2549794) were found to have significantly different effect sizes between the two disease groups tested against healthy controls.
Microarray genotyping was used to perform the experiments because it is cheap, and can be used in a high throughput way to accurately assay many variants across the genome. Other alternates like sequencing are too expensive and single variant testing is not appropriate when many thousands of variants need to be assayed.
The thesis therefore details extensive investigation of the genetic associations of AS and acute anterior uveitis. The associations at genome wide level are likely to be robust true findings, however the associations reported at a suggestive level of significance require replication. In the conclusions chapter the implications of the associations, limitations of the research and future directions are explored. In summary this thesis reports new genetic associations at both genome wide and a suggestive level of significance in AS and acute anterior uveitis.