Introduction: Canadian First Nations experience a significantly higher rate of Mycobacterium tuberculosis (MTB) infection than non-Indigenous Canadians. Th17 cells are a subset of CD4+ T cells that are distinguished by their production of Interleukin-17A (IL-17A), an important cytokine for defense against mycobacteria. IL-17 is a primary contributor to the formation and stabilization of the lung granuloma, a biological containment vessel to protect the host from tuberculosis (TB). Past research with First Nations people has identified single nucleotide polymorphisms (SNPs) in the Th1 and Th2 immune pathways may affect their disease risk. However, SNPs in key Th17 related genes and the P2RX7 gene have not been explored in First Nations despite their important role against infectious diseases. Hypothesis: This research hypothesizes that distinct First Nations groups (Dene, Cree and Saulteaux) will have a different frequencies of SNPs in the key Th17 immunity related genes (IL-17A, IL-17AR, IL-23R, and IFN-γR) and the P2RX7 gene, as compared to a non-Indigenous Canadian group. Methods: SNP profiles (IL-17A rs2275913, IL-17RA rs4819554, IL-23R rs10889677, IFN-γR rs2234711 and P2RX7 rs3751143) were identified through literature research and the NCBI database was used for identifying gene motifs, primer locations and Restriction Enzyme cut sites. Polymerase Chain Reaction and Restriction Fragment Length Polymorphism analysis was performed on and visualized on agarose gel to determine specific allele frequencies. Four different Manitoba First Nations communities; the Northern Dene (Dene 1 N=69. Dene 2 N=52), Central Cree (N=46), and Southern Saulteaux (N=56), participated in this research and their SNP profiles were compared to a non-Indigenous Canadian cohort (N=99). Results: Allele frequencies for IL-17A were statistically different for every First Nation community when compared to the non-Indigenous cohort (Dene 1 p=0.0043, Dene 2 p=0.0000, Cree p=0.0001, Saulteaux p=0.0000). Allele frequencies for IL-17RA were statistically different for every First Nation community except Saulteaux when compared to the non-Indigenous cohort (Dene 1 p=0.0000, Dene 2 p=0.0028, Cree p=0.0000). Allele frequencies for IL-23R were statistically different for Dene 1 and Saulteaux community when compared to the non-Indigenous cohort (Dene 1 p=0.0002, Saulteaux p=0.0000). Allele frequencies for IFN-R were statistically different for Cree community when compared to the non-Indigenous cohort (Cree p=0.0026). Allele frequencies for P2RX7 were statistically different for both Dene communities when compared to the non-Indigenous cohort (Dene 1 p=0.0000, Dene 2 p=0.0000). Conclusions: An effective Th17 response is required to bring Th1 cells to infected tissues and to balance inflammatory responses. Functional SNPs may compromise an appropriate immune response and contribute to disease. This study demonstrate that the non-Indigenous population maintained a significantly different genetic profile when compared to the First Nations populations. / October 2016

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/T_H17 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.