Integrating large scale genomics and functional studies to accelerate FSGS/NS discovery

整合大规模基因组学和功能研究以加速 FSGS/NS 发现

• 批准号: 10652318
• 负责人: FRIEDHELM HILDEBRANDT
• 金额: $ 146.61万
• 依托单位: BETH ISRAEL DEACONESS MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-15 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10652318
• 关键词: Acceleration; Address; Affect; Alleles; Animal Model; Biological Assay; Biological Models; Biology; Cells; Classification; Clinical; Collection; Communities; Complex; Copy Number Polymorphism; Data; Defect; Development; Disease; Disease model; Enhancers; Etiology; Focal and Segmental Glomerulosclerosis; Future; Gene Frequency; Genes; Genetic; Genetic Transcription; Genetic Variation; Genomics; Genotype; Goals; Heritability; Human; Individual; Informatics; Internet; Kidney; Kidney Diseases; Kidney Failure; Kidney Transplantation; Laboratories; Lead; Medical Genetics; Methods; Modeling; Molecular Structure; Mutate; Mutation; Nephrotic Syndrome; Outcome; Pathogenicity; Patients; Penetrance; Phenotype; Prevalence; Reagent; Reporting; Research; Research Personnel; Risk; SNP array; Sample Size; Single Nucleotide Polymorphism; Site; Standardization; Steroid therapy; Steroid-resistant idiopathic nephrotic syndrome; System; Technology; Test Result; Testing; Therapeutic; Variant; Work; Zebrafish; aggregation database; analytical method; cohort; data integration; data resource; diagnostic accuracy; diagnostic tool; empowerment; exome; exome sequencing; gene discovery; gene interaction; genetic disorder diagnosis; genetic profiling; genetic testing; genetic variant; genome sequencing; genome-wide; human model; improved; induced pluripotent stem cell; insertion/deletion mutation; novel; nutritional supplementation; parallelization; predicting response; promoter; response; web portal

SUMMARY The four lead investigators of this project have assembled ~10,000 patients with focal and segmental glomerulosclerosis (FSGS) and steroid-resistant nephrotic syndrome (SRNS). With this largest ever FSGS/NS cohort assembled, the vast majority whom have already undergone genome-wide sequencing, we propose a collaborative effort to understand the genetic basis of this disease. The increasing number of identified genes that can cause FSGS/SRNS when altered shows that these phenotypes are genetically highly complex. Understanding the genetic basis of FSGS and NS is important: (1) Work to date has been the major driver in understanding the molecular structure of the glomerulus; (2) Genetic diagnosis affects therapy: some mutations predict lack of response to steroid therapies, others predict response to nutritional supplementation; (3) Genetics affects renal transplant planning and outcome. Major gaps remain: (1) Most FSGS/NS cases still are genetically unresolved; (2) The basis of disease is complex and involves the contribution of different variants across the spectrum of allelic frequency and penetrance; (3) Our ability to declare genetic causality at the single-patient level is limited; (4) Therapeutic options are limited. Thus, we will use this large cohort and new analytic methods to address these gaps. We will functionally characterize many of the new alleles and new FSGS genes that we discover. We will develop and distribute reagents, including patient-derived iPS cells. We will create a database by aggregating exome and genome sequencing data from our patients, and make this data available via web browser to assist the research community. We plan to: Aim 1: Understand the spectrum of rare genetic variation that causes (or increases risk of) FSGS and NS in humans. By leveraging large sample sizes, we can use approaches that are not otherwise powerful enough for disease gene identification. We will discover novel genes associated with FSGS/NS to identify highly penetrant variants (including burden tests of rare sequence changes and copy-number variants), define the spectrum of SNV and structural variants in known FSGS/NS genes, and identify glomerular genes co-expressed with disease-related genes. Aim 2: Define functional effects of disease-associated variants. We will test effects of variants/mutations in cell-based assays, develop new zebrafish models by mutating FSGS/NS genes, and generate a panel of iPS cells from patients with FSGS/NS-associated mutations. Aim 3: We will bring together all of our genotyping data, generated from SNP arrays, WES, and WGS, to build and maintain a publicly available variant browser, the “Nephrotic Syndrome Genomic Portal” (NSGP). NSGP will include allele frequency data, functional classification, and clinical correlates for FSGS/NS. We will summarize, at a site- level, SNVs, insertion-deletions, structural variants (CNV) observed in our FSGS/NS cohort and provide quality metrics of variants reported. NSGP will also have the capability to accept and incorporate data from other investigators and clinical genetics laboratories.

摘要该项目的四名首席调查人员已经收集了约10,000名患者 节段性肾小球硬化(FSGS)和激素抵抗型肾病综合征(SRNS)。拥有这个最大的 曾经聚集过的FSGS/NS队列，其中绝大多数已经进行了全基因组测序， 我们建议进行合作努力，以了解这种疾病的遗传基础。数量不断增加的 经鉴定的可引起FSGS/SRNS的基因改变后表明，这些表型具有高度的遗传性 很复杂。了解FSGS和NS的遗传基础是重要的：(1)到目前为止的工作一直是主要的 了解肾小球分子结构的驱动力；(2)基因诊断影响治疗：一些 突变预示着对类固醇治疗缺乏反应，其他人则预示着对营养补充的反应； (3)遗传因素影响肾移植的计划和结果。主要差距仍然存在：(1)大多数FSGS/NS病例仍然 是遗传上无法解决的；(2)疾病的基础很复杂，涉及不同的 等位基因频率和外显率范围内的变异；(3)我们在 单一患者水平有限；(4)治疗选择有限。因此，我们将利用这一大群人 填补这些差距的新分析方法。我们将从功能上描述许多新的等位基因和 我们发现的新的FSGS基因。我们将开发和分发试剂，包括患者来源的iPS细胞。 我们将通过汇总患者的外显子组和基因组测序数据来创建一个数据库，并使 这些数据可通过网络浏览器获得，以协助研究社区。我们计划：目标1：了解 导致(或增加)人类FSGS和NS风险的罕见遗传变异的谱系。通过利用 大样本量，我们可以使用对疾病基因来说不够强大的方法 身份证明。我们将发现与FSGS/NS相关的新基因，以识别高渗透性变异 (包括罕见序列变化和拷贝数变异的负荷检验)，定义SNV和 已知FSGS/NS基因的结构变异，并鉴定与疾病相关的肾小球基因共表达 基因。目的2：确定疾病相关变异的功能效应。我们将测试其效果 细胞分析中的变异/突变，通过突变FSGS/NS基因开发新的斑马鱼模型 从患有FSGS/NS相关突变的患者中产生一组iPS细胞。目标3：我们将团结在一起 我们所有的基因分型数据，从SNP阵列、WES和WGS产生，以建立和维护一个公共 可用的变体浏览器，“肾病综合征基因组门户”(NSGP)。NSGP将包括等位基因 FSGS/NS的频率数据、功能分类和临床相关性。我们将在一个网站上总结- 水平、SNV、插入-缺失、结构变异(CNV)在我们的FSGS/NS队列中观察到，并提供质量 报告的变体的指标。NSGP还将能够接受和合并来自其他 研究人员和临床遗传学实验室。