Regulatory T cells (T(regs)) are crucial in the maintenance of the immune tolerance and seem to have an important role in systemic sclerosis (SSc). The interleukin 2 receptor α (IL2RA) is an important T(reg) marker, and polymorphisms of IL2RA gene are associated with a number of autoimmune diseases. Therefore, we aimed to investigate for the first time the association of the IL2RA locus in SSc. For this purpose, a total of 3023 SSc patients and 2735 matched healthy controls, from six European Caucasian cohorts, were genotyped for the IL2RA gene variants rs11594656, rs2104286 and rs12722495 using the TaqMan allelic discrimination technology. The overall meta-analysis reached statistical significance when the three polymorphisms were tested for association with SSc, the limited subtype (lcSSc) and anti-centromere auto-antibodies (ACAs). However, no significant P-values were obtained when the ACA-positive patients were removed from the SSc and lcSSc groups, suggesting that these associations rely on ACA positivity. The strongest association signal with ACA production was detected for rs2104286 (P(FDR)=2.07 × 10(-4), odds ratio=1.30 (1.14-1.47)). The associations of rs11594656 and rs12722495 were lost after conditioning to rs2104286, and allelic combination tests did not evidence a combined effect, indicating that rs2104286 best described the association between IL2RA and ACA presence in SSc.
"Existing evidence suggests that a single locus may contain variants that predispose to any one of multiple diseases, e.g., the nonsynonymous C1858T SNP in PTPN22 is associated with rheumatoid arthritis and T1D [Barrett et al., 2009; Stahl et al., 2010], or distinct variants that predispose to different diseases, e.g., distinct variants in IL2RA are associated with T1D and multiple sclerosis [Maier et al., 2009; Martin et al., 2012]. We used the proportional colocalisation approach outlined above to examine the disease signals for the autoimmune thyroid diseases HT and GD from a recent dense genotyping study [Cooper et al., 2012]. "
[Show abstract][Hide abstract] ABSTRACT: Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions. Formal statistical colocalisation testing of individual regions requires selection of a set of SNPs summarising the association in a region. We show that the SNP selection method greatly affects type 1 error rates, with published studies having used methods expected to result in substantially inflated type 1 error rates. We show that either avoiding variable selection and instead testing the most informative principal components or integrating over variable selection using Bayesian model averaging can help control type 1 error rates. Application to data from Graves' disease and Hashimoto's thyroiditis reveals a common genetic signature across seven regions shared between the diseases, and indicates that in five of six regions associated with Graves' disease and not Hashimoto's thyroiditis, this more likely reflects genuine absence of association with the latter rather than lack of power. Our examination, by simulation, of the performance of colocalisation tests and associated software will foster more widespread adoption of formal colocalisation testing. Given the increasing availability of large expression and genetic association datasets from disease-relevant tissue and purified cell populations, coupled with identification of regulatory sequences by projects such as ENCODE, colocalisation analysis has the potential to reveal both shared genetic signatures of related traits and causal disease genes and tissues.
[Show abstract][Hide abstract] ABSTRACT: Systemic sclerosis (SSc) is a severe connective tissue disorder characterized by extensive fibrosis, vascular damage, and autoimmune events. During the last years, the number of genetic markers convincingly associated with SSc has exponentially increased. In this report, we aim to offer an updated review of the classical and novel genetic associations with SSc, analyzing the firmest and replicated signals within HLA and non-HLA genes, identified by both candidate gene and genome-wide association (GWA) studies. We will also provide an insight into the future perspectives and approaches that might shed more light into the complex genetic background underlying SSc. In spite of the remarkable advance in the field of SSc genetics during the last decade, the use of the new genetic technologies such as next generation sequencing (NGS), as well as the deep phenotyping of the study cohorts, to fully characterize the genetic component of this disease is imperative.
Human Genetics 01/2012; 131(7):1023-37. DOI:10.1007/s00439-011-1137-z · 4.82 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The last decade has seen enormous progress in understanding genetic associations of systemic sclerosis to explain the observed heritability. This review highlights the most recent findings and places them in the context of proposed functional roles.
Over 30 genes and gene regions have now been identified as scleroderma susceptibility loci. These include both human leukocyte antigen (HLA) and non-HLA genes, most of which involve immune-related pathways and modifiers of immune function. Many of these associations have also been reported in other systemic autoimmune diseases and suggest that there are multiple autoimmunity genes resulting in disease occurrence.
In spite of these advances, only a small proportion of the heritability of systemic sclerosis has been explained. Ongoing studies include fine mapping and sequencing studies to identify causal variants, whereas other studies focus on functional consequences of these variants in order to identify the link between these genetic variants and disease susceptibility. Such knowledge should lead to more targeted and effective treatment in this disease.
Current opinion in rheumatology 11/2012; 24(6):677-84. DOI:10.1097/BOR.0b013e328358575b · 4.89 Impact Factor
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