Rare Variants and Risk of Type 1 Diabetes

描述(申请人提供)：1型糖尿病(T1D)是一种复杂的自身免疫性疾病，由多种遗传和环境风险因素引起，可影响多达300名儿童中的1名。2001年，1型糖尿病遗传学联合会(T1DGC)成立，其目标是进行大规模的基因研究，以确定基因组中导致T1D风险的区域，并向更广泛的科学界提供收集的数据和生物样本。T1DGC已经非常成功地使用(A)候选基因、(B)MHC中的变异、(C)全基因组连锁和(D)全基因组关联扫描(GWAS)对T1D进行了最强有力的研究。从我们对16,000多个病例和对照的荟萃分析中，报告了18个新发现的具有全基因组意义的基因座(Pd5×10-8)，包括在独立的4,267例病例、4,463个对照和2,319个家系中的复制证据。这使得T1D基因座的总数达到42个。我们现在已经对新的18个基因座进行了后续的基因分型，并在所有已知的T1D基因座上进行了密集的SNP定位(使用免疫芯片)。我们在大多数这些基因座上发现了单一的T1D候选基因。通过对常见遗传变异的分析，来自GWAs的基因座解释了T1D总遗传易感性的不到15%(仅次于MHC中基因贡献的50%)。残留的遗传风险(“缺失遗传性”)可能是由于在基因编码区发现的罕见变异所致。这些罕见的编码变体很可能是功能性的，对风险有很大影响。与常见的变异体不同，发现罕见的功能变异体需要对这些编码和调控区域进行DNA测序。测序工作，甚至编码区(外显子组)的测序工作都是以巨大的成本进行的。为了测试T1D与罕见变异的关联，已经设计了一种从12,000多个人类外显子中提取的基因分型阵列(ExomeChip)。这种定制的阵列将允许以较低的成本对大量样本进行基因分型，从而测试罕见的变异。ExomeChip包含约200,000个非同义、无义和剪接位点变体，以及100,000个用于附加内容的变体(包括MHC变体)。这项赠款申请的主要目的是通过以下方式发现导致T1D风险的新的遗传风险因素：1)在2,500个受T1DGC影响的同胞对(ASP)家族中进行ExomeChip基因分型；2)对ExomeChip数据进行分析(单SNP和负荷测试)，以发现其功能显著的变异影响T1D风险的新基因；以及3)通过在约7,000个T1D病例和~7,000个对照中进行定向测序，复制这些新结果。我们将整合现有的数据(HLA分型、免疫芯片、CNV、外芯片)，以提供与T1D风险相关的罕见、常见和结构变异的全面分析。这些发现将导致新的病因学途径和T1D预测、预防和治疗的途径。

DESCRIPTION (provided by applicant): Type 1 diabetes (T1D) is a complex autoimmune disorder that arises from the action of multiple genetic and environmental risk factors and can affect up to 1 in 300 children. In 2001, the Type 1 Diabetes Genetics Consortium (T1DGC) was established with the goals of conducting large-scale genetic studies to identify regions in the genome that contribute to T1D risk and making available the assembled data and biospecimens to the broader scientific community. The T1DGC has been highly successful conducting the most robustly powered studies of T1D using (a) candidate genes, (b) variants in the MHC, (c) genome-wide linkage, and (d) genome-wide association scan (GWAS). From our GWAS meta-analysis of over 16,000 cases and controls, 18 newly identified loci were reported at genome-wide significance (P d 5 x 10-8), including replication evidence in an independent set of 4,267 cases, 4,463 controls and 2,319 families. This brought the total number of T1D loci to 42. We have now conducted follow-up genotyping of the novel 18 loci, and conducted dense SNP mapping (using the ImmunoChip) in all known T1D loci. We have discovered a single T1D candidate gene in the majority of these loci. The loci from GWAS discovered through analysis of common genetic variants explain less than 15% of the total genetic liability of T1D (after the 50% contributed by genes in the MHC). The residual genetic risk ("missing heritability") may be due to rare variants that are found in coding regions of genes. These rare coding variants are likely to be functional with large effects on risk. Unlike common variants, DNA sequencing of these coding and regulatory regions is required for discovery of rare functional variants. The sequencing effort, even of the coding regions (the "exome") is performed at significant cost. For testing association of T1D with rare variants, a genotyping array (the ExomeChip) has been designed from over 12,000 human exomes. This custom array will permit testing of rare variants by genotyping large numbers of samples at reduced cost. The ExomeChip contains ~200,000 non-synonymous, non-sense, and splice-site variants, as well as 100,000 variants for additional content (including MHC variants). The primary aims of this grant application are to discover novel genetic risk factors that contribute to risk of T1D by 1) conducting ExomeChip genotyping in a well-characterized collection of 2,500 T1DGC affected sib pair (ASP) families; 2) performing analyses of the ExomeChip data (both single SNP and burden tests) in order to discover new genes whose functionally significant variants influence risk to T1D; and 3) replicating these novel results by targeted sequencing in ~7,000 T1D cases and ~7,000 controls. We will integrate existing data (HLA typing, ImmunoChip, CNV, ExomeChip) to provide a comprehensive analysis of rare, common, and structural variation associated with T1D risk. These findings should lead to novel pathways of etiology and avenues for T1D prediction, prevention and therapy.