Genome-Wide Association and Exon Sequencing Study in IPF

描述（由申请人提供）：该申请涉及广泛的挑战领域（08）基因组学和特定挑战主题，08- hl -101*“通过应用靶向DNA捕获和大规模平行测序技术，然后对来自大型表型良好人群的DNA样本进行选择性基因分型，确定与心脏，肺和血液疾病相关的因果遗传变异”。特发性肺纤维化（IPF）是一种进行性无法治愈的肺部疾病。IPF避开了可能为新治疗方法提供靶点的因果遗传决定因素。本研究的目的是在一个大型队列中使用全基因组关联研究（GWAS）小组来确定导致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。为实现这一目标，我们制定了以下具体目标：建立超过700名IPF患者的联合队列，并对450名IPF患者进行全基因组关联研究（GWAS）。待验证的假设是，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700名IPF患者样本集的手动和电子管理数据库中建立具有临床意义的疾病表型定义，然后使用Affymetrix SNP 6.0 GeneChip(R)对450名IPF患者进行完整的GWAS，并将GWAS基因型和表型数据存储在NIH数据库中dbGap。具体目标2。通过表型严重程度和进展速度对遗传变异进行标准和新颖的分析。有待检验的假设是，遗传因素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基因型对照GWAS数据来确定与IPF相关的snp，并通过可用的探针评估拷贝数多态性，并测试与IPF表型的关联，并确定在死亡率高的“快速进展”IPF受试者与“缓慢”IPF受试者、严重程度等级或其他临床结果测量之间，相关变异的频率是否不同。执行外显子范围靶向DNA测序和基因分型，以验证GWAS相关的遗传变异，并发现白种人和非裔美国人IPF的功能变异。需要验证的假设是，对具有不同民族和种族背景和严重程度队列的受试者进行外显子全序列测序，将允许识别与IPF相关的因果/功能变异。我们将在200名重复IPF患者队列中使用选择性SNP阵列复制最重要的关联，然后使用Illumina 454技术对160名高加索人和非裔美国人的48个基因进行外显子全域测序，并对亚目标b中发现的外显子变异进行统计分析。我们期望完成全基因组关联研究，使用临床有意义的表型加上外显子全域重测序将导致鉴定促进IPF发展的基因和特定的遗传变异。然后，这可以作为指导，导致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.