Genome-Wide Association and Exon Sequencing Study in IPF

描述(申请人提供)：本申请涉及广泛的挑战领域(08)基因组学和特定的挑战主题，08-HL-101*“通过应用定向DNA捕获和大规模平行测序技术，然后对大量表型良好的人群的DNA样本进行选择性基因分型，识别与心脏、肺和血液疾病相关的因果遗传变异”。特发性肺纤维化(IPF)是一种进展性的不可治疗的肺部疾病。IPF避开了可能为新的治疗方法提供靶点的因果遗传决定因素。这项拟议研究的目的是利用全基因组关联研究(GWAS)小组，在一个大规模的符合队列的队列中，确定导致IPF风险的因果遗传变异。每个DNA样本都附有详细的表型数据。为了实现这一目标，我们有以下具体目标：具体目标1.建立700多名IPF患者的联合队列，并在450名IPF患者中进行基因组广泛关联研究(Gwas)。需要检验的假设是，遗传因素影响个体对IPF的易感性。为了实现这一目标，我们将在合并的手动和电子精选数据库中为疾病表型建立具有临床意义的定义，该数据库包含所有700名IPF患者的协作组患者样本，然后使用Affymetrix SNP 6.0 GeneChip(R)对450名IPF患者进行完整的GWAS检查，并将GWA型和表型数据存储在DBGaP的NIH储存库中。具体目标2.根据表型、严重程度和进展速度对遗传变异进行标准和新的分析。需要检验的假设是，遗传因素会影响疾病的预后和严重程度。为了实现这一目标，我们将利用公开保存的GWAS型对照数据来确定与IPF相关的SNPs，并通过可用的探针评估拷贝数多态，并测试与IPF表型的关联，并确定相关变异在高死亡率的快速进展型IPF受试者和那些具有高死亡率、严重程度或其他临床结果指标的受试者之间是否存在不同的频率。要检验的假设是，对具有不同民族和种族背景以及严重程度队列的受试者进行外显子范围的测序将允许识别与IPF相关的因果/功能变异。我们将利用选择性SNP阵列在200名重复的IPF患者队列中复制最显著的关联，然后使用Illumina 454技术对160名高加索人和非裔美国人的48个基因进行外显子范围的测序，并对子目标b中发现的外显子变异进行统计分析。我们预计，使用具有临床意义的表型与外显子范围的重新测序相结合的全基因组关联研究的完成将导致识别与IPF的发展有关的基因和特定的遗传变异。然后，这可以作为指南，引导人们找到预防和治疗这种致命疾病的新方法。

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (08) Genomics and Specific Challenge Topic, 08-HL-101* "Identify causal genetic variants associated with heart, lung, and blood diseases by application of targeted DNA capture and massively parallel sequencing technologies followed by selective genotyping of DNA samples from large well-phenotyped populations". Idiopathic Pulmonary fibrosis (IPF) is a progressive untreatable lung disease. IPF has eluded causal genetic determinants that may provide targets for novel therapeutic approaches. The objective of this proposed research is to identify causal genetic variants contributing to risk of IPF using a Genome-wide association studies (GWAS) panel in a large complied cohort. Each DNA sample is accompanied by detailed phenotypic data. To meet this objective we have the following specific aims: Specific Aim 1. To establish a combined cohort of over 700 IPF patients and perform a Genome Wide Association Study (GWAS) in 450 subjects with IPF. The hypothesis to be tested is that inheritable genetic factors affect individual susceptibility of IPF. To accomplish this we will establish clinically meaningful definitions for disease phenotypes in a merged manually and electronically curated database of all 700 collaborator patient sample sets of IPF patients and then perform a complete a GWAS using Affymetrix SNP 6.0 GeneChip(R) in 450 IPF patients and deposit the GWAS genotype and phenotype data in the NIH repository in dbGap. Specific Aim 2. Conduct both standard and novel analyses in genetic variation by phenotypes severity and rapidity of progression. The hypothesis to be tested is that inheritable genetic factors influence prognosis and severity of the disease. To accomplish this we will determine SNPs associated with IPF utilizing publicly deposited genotyped control GWAS data and evaluate copy number polymorphisms via available probes, and test for association with IPF phenotypes and determine if the associated variants differ in frequency between subjects with "rapidly progressive" IPF with high mortality versus those with "slow" IPF, severity grade or other clinical outcome measures Specific Aim 3. Perform Exon-Wide targeted DNA sequencing and genotyping to validate the GWAS associated genetic variants and to discover functional variations in Caucasians and African Americans with IPF. The hypothesis to be tested is that Exon-Wide sequencing of subjects with different ethnic and racial backgrounds and severity cohorts will allow the identification of causal/functional variants associated with IPF. We will replicate the most significant associations with a selective SNP array in a replicate IPF patient cohort of 200 subjects and then perform Exon-wide sequencing of 48 genes in 160 Caucasian and African American subjects using Illumina 454 technology and conduct a statistical analysis of exon variants discovered in sub- aim b. We expect that completion of a genome-wide association study using clinically meaningful phenotypes coupled to exon-wide re-sequencing will lead to identification of the genes and the specific genetic variants that contribute to the development of IPF. This can then be used as guide to lead to new approaches for preventing and treating this deadly disease.