Deep Re-Sequencing of Rheumatoid Arthritis Risk Loci

类风湿关节炎风险位点的深度重测序

• 批准号: 8119549
• 负责人: ROBERT M PLENGE
• 金额: $ 24.26万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8119549
• 关键词: Alleles; Amino Acid Sequence; Autoimmune Diseases; Biological; Candidate Disease Gene; Chromosome Mapping; Code; Collection; Computing Methodologies; Crohn' s disease; DNA; Development; Diagnosis; Disease; Disease Association; Disease Pathway; Environment; Exons; Frequencies; General Population; Genes; Genetic; Genome; Genotype; Goals; Haplotypes; Individual; Institutes; Insulin-Dependent Diabetes Mellitus; Methods; Morphologic artifacts; Mutation; Nature; Non-Insulin-Dependent Diabetes Mellitus; PTPN22 gene; Pathogenesis; Pathway interactions; Patient Care; Peptide Sequence Determination; Positioning Attribute; Process; Property; Proteins; Rare Diseases; Research Design; Rheumatoid Arthritis; Risk; Sampling; Scientist; Series; Symptoms; Technology; Testing; Variant; base; bone; case control; cost effective; disorder risk; experience; gene function; genome wide association study; improved; insight; next generation; public health relevance; theories

DESCRIPTION (provided by applicant): Genome-wide association studies (GWAS) in rheumatoid arthritis (RA) have led to the identification of more than 25 regions of the genome that contribute to risk of disease (RA risk loci). Despite this exciting progress at gene mapping, these alleles explain <20% of the overall variation in RA risk, indicating that many more risk alleles remain to be identified. In the current application, we propose to re-sequence the protein-coding portion of candidate genes from 25 RA risk loci to search for rare functional mutations. If a rare disease-associated mutation is identified, then this gene is almost certainly the causal gene. These rare functional mutations will provide an opportunity to study fundamental mechanisms of RA pathogenesis. In this application, we hypothesize that rare functional alleles contribute to risk of RA in genes that also harbor independent common alleles identified by GWAS. To test this hypothesis, we will implement next-generation sequencing technology, which provides a cost-effective approach to re- sequence candidate genes. Aim 1: Re-sequence the coding exons of 27 biological candidate genes in 750 RA cases and 750 matched controls using next-generation sequencing technology. We will identify all common and rare alleles using a robust sequencing pipeline recently developed by our colleagues at the Broad Institute. Aim 2: Genotype all functional alleles in the same 750 cases and 750 controls, and conduct an association study with disease risk. We will genotype all putative functional mutations in the same samples to confirm the sequence calls and to determine the genotype of each subject. We will test for association with RA risk in two ways: an allele-based test and a gene-base test. Aim 3: We will replicate our findings in additional samples. If our allele-based test identifies disease-associated functional alleles that are low frequency yet segregate on an ancestral haplotype, then we will replicate the finding by genotyping the rare allele in >10,000 additional case-control samples. If our gene-based test identifies a collection of disease-associated rare alleles that are private to individuals (i.e., are of recent ancestral origin, do not segregate on ancestral haplotypes), then we will re-sequence the coding exons of that gene in an additional 1,500 cases and 1,500 controls. We have assembled a team of scientists uniquely positioned to conduct all aspects of the project. Our studies will be conducted within a scientific environment that appreciates the power of next-generation sequencing, without underestimating it's technical and analytical challenges. PUBLIC HEALTH RELEVANCE: A long-term goal of understanding the genetic basis of rheumatoid arthritis is to improve care of patients with this common and debilitating disease. In theory, identifying specific pieces of DNA ("alleles") should aid in diagnosing a treatable condition either prior to onset of symptoms, or early in the course of disease before bone destruction occurs. In addition, genetics should provide insight into important steps of the disease pathway, allowing for the development of new therapies that target these pathways in at-risk individuals.

描述（由申请人提供）：类风湿性关节炎 (RA) 的全基因组关联研究 (GWAS) 已鉴定出超过 25 个与疾病风险有关的基因组区域（RA 风险位点）。尽管在基因图谱方面取得了令人兴奋的进展，但这些等位基因解释了 RA 风险总体变异的 <20%，这表明还有更多的风险等位基因有待识别。在当前的应用中，我们建议对 25 个 RA 风险位点的候选基因的蛋白质编码部分进行重新测序，以寻找罕见的功能突变。如果发现了与罕见疾病相关的突变，那么该基因几乎肯定是致病基因。这些罕见的功能突变将为研究 RA 发病机制的基本机制提供机会。在本申请中，我们假设罕见的功能性等位基因会导致基因中的 RA 风险增加，而这些基因也含有 GWAS 鉴定出的独立的常见等位基因。为了检验这一假设，我们将实施下一代测序技术，该技术提供了一种经济高效的方法来对候选基因进行重新测序。目标 1：使用新一代测序技术对 750 个 RA 病例和 750 个匹配对照中 27 个生物候选基因的编码外显子进行重新测序。我们将使用布罗德研究所的同事最近开发的强大测序流程来识别所有常见和罕见的等位基因。目标 2：对相同的 750 个病例和 750 个对照中的所有功能等位基因进行基因分型，并进行与疾病风险的关联研究。我们将对同一样本中所有假定的功能突变进行基因分型，以确认序列调用并确定每个受试者的基因型。我们将通过两种方式测试与 RA 风险的关联：基于等位基因的测试和基于基因的测试。目标 3：我们将在更多样本中复制我们的发现。如果我们基于等位基因的测试识别出频率较低但在祖先单倍型上分离的疾病相关功能等位基因，那么我们将通过在超过 10,000 个额外病例对照样本中对罕见等位基因进行基因分型来复制这一发现。如果我们的基于基因的测试识别出一系列与疾病相关的罕见等位基因，这些等位基因是个体专有的（即，具有最近的祖先起源，不根据祖先单倍型进行分离），那么我们将在另外 1,500 个病例和 1,500 个对照中对该基因的编码外显子进行重新测序。 我们组建了一支独特的科学家团队来开展该项目的各个方面。 我们的研究将在重视下一代测序力量的科学环境中进行，同时不会低估其技术和分析挑战。 公众健康相关性：了解类风湿关节炎遗传基础的长期目标是改善对患有这种常见且使人衰弱的疾病的患者的护理。理论上，识别特定的 DNA 片段（“等位基因”）应该有助于在症状出现之前或在骨质破坏发生之前的病程早期诊断可治疗的病症。此外，遗传学应该提供对疾病途径的重要步骤的深入了解，从而允许开发针对高危个体的这些途径的新疗法。