Rare Variants and Risk of Type 1 Diabetes

描述（由申请人提供）：1型糖尿病（T1 D）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的作用引起，最多可影响1/300的儿童。2001年，1型糖尿病遗传学联盟（T1 DGC）成立，其目标是进行大规模遗传研究，以确定基因组中导致T1 D风险的区域，并向更广泛的科学界提供收集的数据和生物标本。T1 DGC已经非常成功地使用（a）候选基因，（B）MHC变体，（c）全基因组连锁和（d）全基因组关联扫描（GWAS）进行了最有力的T1 D研究。从我们对超过16，000例病例和对照的GWAS荟萃分析中，报告了18个新发现的基因座具有全基因组显著性（P d 5 x 10-8），包括4，267例病例、4，463例对照和2，319个家族的独立组中的复制证据。这使得T1 D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基因分型，并在所有已知的T1 D基因座中进行了密集的SNP作图（使用免疫芯片）。我们已经发现了一个单一的T1 D候选基因在大多数这些位点。通过分析常见遗传变异发现的GWAS基因座解释了T1 D总遗传易感性的不到15%（在MHC基因贡献的50%之后）。剩余遗传风险（“缺失遗传性”）可能是由于在基因编码区发现的罕见变异。这些罕见的编码变异可能对风险有很大的影响。与常见变异不同，这些编码和调控区的DNA测序是发现罕见功能变异所必需的。测序工作，甚至是编码区（“外显子组”）的测序工作都是以相当高的成本进行的。为了测试T1 D与罕见变异的关联，已经从超过12，000个人类外显子组设计了基因分型阵列（ExomeChip）。这种定制的阵列将允许以较低的成本通过对大量样本进行基因分型来测试罕见变异。ExomeChip包含约200，000个非同义、无义和拼接位点变体，以及100，000个附加内容变体（包括MHC变体）。这项资助申请的主要目的是通过以下方式发现导致T1 D风险的新遗传风险因素：1）在2，500个T1 DGC影响的同胞对（ASP）家庭的充分表征的集合中进行ExomeChip基因分型; 2）对ExomeChip数据进行分析。（单SNP和负荷测试），以发现其功能显著变异影响T1 D风险的新基因;以及3）通过靶向测序在约7，000例T1 D病例和约7，000例对照中复制这些新结果。我们将整合现有的数据（HLA分型，免疫芯片，CNV，ExomeChip），以提供与T1 D风险相关的罕见，常见和结构变异的综合分析。这些发现将为T1 D的预测、预防和治疗带来新的病因学途径和途径。 公共卫生相关性：1型糖尿病（T1 D）是一种常见的自身免疫性疾病，由遗传和非遗传因素介导的胰腺B细胞破坏引起。我们在基因组中发现了40多个与常见遗传变异有显著关联的区域，并确定了最有可能的候选基因。尽管取得了这一成功，但遗传风险仍然没有得到解决，这可能是由于在基因编码区发现了罕见的变异。我们建议使用定制的基因分型阵列（ExomeChip）来发现由于罕见变异而导致的T1 D风险所涉及的基因和途径，最终目标是开发T1 D预测，预防和治疗的新途径。

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. PUBLIC HEALTH RELEVANCE: Type 1 diabetes (T1D) is a common autoimmune disease that results from pancreatic b cell destruction, mediated by both genetic and non-genetic factors. We discovered over 40 regions in the genome with significant associations with common genetic variants and have identified the most likely candidate genes. Despite this success, there remains genetic risk unresolved, likely due to rare variants found in coding regions of genes. We propose to use a custom genotyping array (the ExomeChip) to discover the genes and pathways involved in T1D risk due to rare variants, with an ultimate goal of developing novel avenues for T1D prediction, prevention and therapy.