Genetics of ankylosing spondylitis
Keywords: inflammatory bowel disease
TASC
immunology
case control study
candidate gene study
HLA-B27
inflammation
1000 Genomes Project
sequencing
imputation accuracy
MACH
C-Alpha
interleukin 23 receptor
rheumatology
tumour necrosis factor receptor 1
Crohn's disease
polyphred
PCR
WTCCC2
psoriasis
statistical power
uveitis
endoplasmic reticulumn associated protease 2
Genetic Association Study
low frequency variants
ERAP1
GRANVIL
TNFRSF1A
endoplasmic reticulumn associated protease 1
spine
ulcerative colitis
anti-TNF
CCRaVAT
meta-analysis
TNFR1
stratified analysis
polymerase chain reaction
logistic regression
genetics
ankylosing spondylitis
Genomewide Association study
iritis
ERAP2
GWAS
TH-17 pathway
rare variants
variant discovery
Mach2Dat
imputation
HapMap Project
IL23R

Ankylosing spondylitis (AS) is a common inflammatory arthritis of the spine and other affected joints, which is highly heritable, being strongly influenced by the HLA-B27 status, as well as hundreds of mostly unknown genetic variants of smaller effect. The aim of my research was to confirm some of the previously observed genetic associations and to identify new associations, many of which are in biological pathways relevant to AS pathogenesis, most notably the IL-23/TH17 axis (IL23R) and antigen presentation (ERAP1 and ERAP2). Studies presented in this thesis include replication and refinement of several potential associations initially identified by earlier GWAS (WTCCC-TASC, 2007 and TASC, 2010). I conducted an extended study of IL23R association with AS and undertook a meta-analysis, confirming the association between AS and IL23R (non-synonymous SNP rs11209026, p=1.5 x 10-9, OR=0.61). An extensive re-sequencing and fine mapping project, including a meta-analysis, to replicate and refine the association of TNFRSF1A with AS was also undertaken; a novel variant in intron 6 was identified and a weak association with a low frequency variant, rs4149584 (p=0.01, OR=1.58), was detected. Somewhat stronger associations were seen with rs4149577 (p=0.002, OR=0.91) and rs4149578 (p=0.015, OR=1.14) in the meta-analysis. Associations at several additional loci had been identified by a more recent GWAS (WTCCC2-TASC, 2011). I used in silico techniques, including imputation using a denser panel of variants from the 1000 Genomes Project, conditional analysis and rare/low frequency variant analysis, to refine these associations. Imputation analysis (1782 cases/5167 controls) revealed novel associations with ERAP2 (rs4869313, p=7.3 x 10-8, OR=0.79) and several additional candidate loci including IL6R, UBE2L3 and 2p16.3. Ten SNPs were then directly typed in an independent sample (1804 cases/1848 controls) to replicate selected associations and to determine the imputation accuracy. I established that imputation using the 1000 Genomes Project pilot data was largely reliable, specifically for common variants (genotype concordence~97%). However, more accurate imputation of low frequency variants may require larger reference populations, like the most recent 1000 Genomes reference panels. The results of my research provide a better understanding of the complex genetics of AS, and help identify future targets for genetic and functional studies.