Genome-Wide Association and Exon Sequencing Study in IPF

描述（由申请人提供）：本申请解决了广泛的挑战领域（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，然后对来自大量表型良好人群的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）是一种进行性不可治疗的肺部疾病。IPF没有可能为新型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在一个大型的符合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。为了实现这一目标，我们有以下具体目标：具体目标1。建立超过700例IPF患者的联合队列，并在450例IPF受试者中进行全基因组关联研究（GWAS）。待检验的假设是可遗传的遗传因素影响IPF的个体易感性。为了实现这一点，我们将在合并的IPF患者的所有700个合作者患者样本集的手动和电子策划的数据库中建立疾病表型的临床有意义的定义，然后使用Affytek SNP 6.0 GeneChip（R）在450名IPF患者中进行完整的GWAS，并将GWAS基因型和表型数据存款dbGap中的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。有待检验的假设是，可遗传的遗传因素影响疾病的预后和严重程度。为了实现这一点，我们将利用公开存放的基因分型对照GWAS数据确定与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，并确定具有高死亡率的“快速进展”IPF受试者与具有“缓慢”IPF受试者之间相关变体的频率、严重程度等级或其他临床结局指标是否不同。进行全外显子靶向DNA测序和基因分型，以验证GWAS相关遗传变异，并发现白人和非洲裔美国人IPF患者的功能变异。待检验的假设是，具有不同种族和人种背景和严重程度队列的受试者的全外显子测序将允许识别与IPF相关的因果/功能变体。我们将在200例受试者的重复IPF患者队列中复制与选择性SNP阵列的最显著关联，然后使用Illumina 454技术对160例高加索人和非洲裔美国人受试者的48个基因进行外显子全测序，并对子目标B中发现的外显子变体进行统计分析。我们预计，使用临床上有意义的表型结合外显子全范围重新测序完成全基因组关联研究，将有助于识别导致IPF发生的基因和特定遗传变异。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.