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: 7943500
• 负责人: ROBERT M PLENGE
• 金额: $ 25.05万
• 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/7943500
• 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; 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）已经鉴定出超过25个基因组区域与疾病风险相关（RA风险基因座）。尽管在基因定位方面取得了令人兴奋的进展，但这些等位基因解释了RA风险总体变化的<20%，表明仍有更多的风险等位基因有待鉴定。在本申请中，我们建议对来自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。如果一个罕见的疾病相关的突变被确定，那么这个基因几乎肯定是致病基因。这些罕见的功能性突变将为研究RA发病机制提供机会。在本申请中，我们假设罕见的功能性等位基因有助于RA的风险基因，也具有独立的共同等位基因GWAS确定。为了验证这一假设，我们将实施下一代测序技术，该技术提供了一种重新测序候选基因的成本效益方法。目标1：采用新一代测序技术对750例RA病例和750例匹配对照的27个生物学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的测序管道来识别所有常见和罕见的等位基因。目的2：对750例病例和750例对照进行全基因分型，并进行与疾病风险的关联研究。我们将对相同样本中所有推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。我们将以两种方式测试与RA风险的相关性：基于等位基因的测试和基于基因的测试。目标3：我们将在其他样本中复制我们的发现。如果我们的基于等位基因的测试鉴定出低频率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> 10，000个额外的病例对照样本中对罕见等位基因进行基因分型来复制该发现。如果我们基于基因的测试识别出一组与疾病相关的罕见等位基因，这些等位基因是个体独有的（即，是最近的祖先起源，不分离的祖先单倍型），那么我们将重新测序该基因的编码外显子在另外1,500例和1,500对照。 我们已经组建了一个科学家团队，他们具有独特的能力来进行该项目的各个方面。 我们的研究将在一个欣赏下一代测序的力量的科学环境中进行，而不会低估它的技术和分析挑战。 公共卫生关系：了解类风湿性关节炎的遗传基础的长期目标是改善这种常见和衰弱疾病患者的护理。从理论上讲，识别特定的DNA片段（“等位基因”）应该有助于在症状发作之前或在骨破坏发生之前的疾病过程中早期诊断可治疗的疾病。此外，遗传学应该提供对疾病途径重要步骤的洞察，允许开发针对高危个体中这些途径的新疗法。