Structural Genetic Variation in Asthma

哮喘的结构遗传变异

• 批准号: 7841725
• 负责人: Benjamin Alexander Raby
• 金额: $ 83.15万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2012-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7841725
• 关键词: Affect; African American; Asthma; Bioinformatics; Biological; Biological Assay; Candidate Disease Gene; Child; Childhood; Childhood Asthma; Clinical; Complex; Costa Rica; Custom; Cytogenetics; DNA; DNA Resequencing; DNA Sequence Rearrangement; DNA copy number; Data; Development; Diagnostic; Diagnostic tests; Disease; Disease susceptibility; Enzyme-Linked Immunosorbent Assay; Epidemiology; Ethnic Origin; Ethnic group; Family; Gene Expression; Genes; Genetic; Genetic Determinism; Genetic Variation; Genomics; Genotype; Hispanics; Human; Individual; Lead; Messenger RNA; Methods; Molecular Target; Morbidity - disease rate; Not Hispanic or Latino; Nucleotides; Oligonucleotide Microarrays; Parents; Pathogenesis; Phenotype; Population; Predisposition; Prevalence; Proteins; RNA; Research Personnel; Resolution; Risk; Role; Sample Size; Sampling; Single Nucleotide Polymorphism; Statistical Methods; Surveys; Testing; Time; Transcript; United States; Validation; Variant; base; cohort; cost; density; design; follow-up; genetic variant; genome wide association study; genome-wide; high throughput technology; human disease; lymphoblastoid cell line; novel; prognostic; programs; protein expression; public health relevance; structural genomics; therapeutic target; tool

DESCRIPTION (provided by investigator): Copy number variants (CNVs) are structural genetic variants consisting of large DNA segments whose number varies between individuals. The importance of these large-scale gains and losses has only recently been recognized: CNVs are extremely common, represent a large proportion of the total genetic variation, and contribute substantially to phenotypic variation and disease susceptibility. Asthma affects over 17 million people in the U.S. and represents a significant cause of morbidity. Though the cumulative results of more than 20 genome-wide genetic surveys for asthma susceptibility loci have successfully identified several novel asthma genes, none of these prior studies have assessed the role of CNVs in the pathogenesis of asthma. In preliminary studies using a genome-wide, family-based screen of ~500,000 single nucleotide polymorphism genotypes in 400 families with asthma, our group has identified several genomic regions harboring known structural variation that are strongly associated with asthma susceptibility, including several containing previously identified asthma genes. From these preliminary data, we hypothesize that common structural genomic variants confer important susceptibility to asthma prevalence in multiple populations. We propose 4 Specific Aims to test this hypothesis. In Specific Aim 1 we will perform a family-based genome-wide association study in non-Hispanic white families with childhood asthma using high-resolution CNV genotype data generated with Affymetrix SNP6.0 microarrays. We will then technically validate the top 20 asthma- associated CNV regions identified using high-density oligonucleotide arrays and quantitative PCR methods. In Specific Aim 2, we will replicate these associations in three independent asthma cohorts (total sample size ~6000 subjects), including Hispanic white and non-Hispanic black populations. In Specific Aim 3 we will sequence candidate genes and perform follow-up SNP genotyping and association testing in the asthma cohorts to identify asthma-related nucleotide variation in 2 replicated asthma-associated CNV regions. In Specific Aim 4 we will evaluate the impact of asthma-associated CNVs on mRNA gene expression and target protein expression levels for candidate genes residing within or near the asthma-associated CNVs in 180 asthmatics. This project has high potential to identify novel molecular targets critical to the pathobiology of asthma for therapeutic targeting. PUBLIC HEALTH RELEVANCE Structural genetic variants consist of large DNA segments whose number varies between individuals. This project aims to identify structural genetic variation that contributes to the development of asthma. We propose to conduct a genome-wide survey for such variation in a cohort of childhood asthmatics, with follow-up characterization of these regions and replication studies in populations representing the three major ethnic groups in the United States. Defining the genetic determinants of asthma will ultimately lead to the development of novel therapies and diagnostic tests.

描述（由研究者提供）：拷贝数变异（CNV）是由大DNA片段组成的结构遗传变异，其数量在个体之间存在差异。这些大规模的增益和损失的重要性最近才被认识到：CNVs是非常常见的，代表了很大比例的总遗传变异，并大大有助于表型变异和疾病的易感性。在美国，哮喘影响超过1700万人，并且是发病的重要原因。尽管20多个哮喘易感基因位点全基因组遗传学调查的累积结果已经成功地鉴定了几个新的哮喘基因，但这些先前的研究都没有评估CNV在哮喘发病机制中的作用。在400个哮喘家系中，我们对约50万个单核苷酸多态性基因型进行了全基因组、以家族为基础的筛查，初步研究发现，几个基因组区域含有与哮喘易感性密切相关的已知结构变异，包括几个含有先前确定的哮喘基因的区域。从这些初步数据，我们假设，共同的结构基因组变异赋予重要的易感性哮喘患病率在多个群体。我们提出了四个具体目标来检验这一假设。在具体目标1中，我们将使用Affytron SNP 6.0微阵列生成的高分辨率CNV基因型数据，在患有儿童哮喘的非西班牙裔白色家庭中进行基于家庭的全基因组关联研究。然后，我们将在技术上验证使用高密度寡核苷酸阵列和定量PCR方法鉴定的前20个哮喘相关CNV区域。在特定目标2中，我们将在三个独立的哮喘队列（总样本量约6000例受试者）中复制这些相关性，包括西班牙裔白色和非西班牙裔黑人人群。在特定目标3中，我们将对候选基因进行测序，并在哮喘队列中进行随访SNP基因分型和相关性检测，以确定2个重复的哮喘相关CNV区域中的哮喘相关核苷酸变异。在具体目标4中，我们将评估180例哮喘患者中哮喘相关CNVs对mRNA基因表达和靶蛋白表达水平的影响，这些基因位于哮喘相关CNVs内或附近。该项目具有很高的潜力，以确定新的分子靶点的关键哮喘的病理生物学治疗靶向。公共卫生相关性结构遗传变异由大的DNA片段组成，其数量在个体之间变化。该项目旨在确定导致哮喘发展的结构遗传变异。我们建议在一组儿童哮喘患者中进行全基因组调查，对这些区域进行后续表征，并在代表美国三大种族的人群中进行复制研究。确定哮喘的遗传决定因素将最终导致新疗法和诊断测试的发展。