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: 10237944
• 负责人: FRIEDHELM HILDEBRANDT
• 金额: $ 148.2万
• 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/10237944
• 关键词: Address; Affect; Alleles; Animal Model; Biological Assay; Biological Models; Biology; Cells; Classification; Clinical; Collection; Communities; Complex; Copy Number Polymorphism; Data; Databases; Defect; Development; Diagnostic; Disease; Disease Progression; Disease model; Enhancers; Etiology; Focal 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; Structure; System; Technology; Test Result; Testing; Therapeutic; Variant; Work; Zebrafish; analytical method; base; case control; cohort; data resource; diagnostic accuracy; 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; predicting response; promoter; response; tool; 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.

总结该项目的四名主要调查员已组装了约10,000名焦点患者和 节段性肾小球硬化（FSGS）和抗类固醇的肾病综合征（SRNS）。与这个最大的 FSGS/NS队列组装了，绝大多数已经接受了全基因组测序， 我们提出了一项协作努力，以了解该疾病的遗传基础。越来越多的 鉴定出可能引起FSG/SRN的基因发生变化时表明这些表型通常是高度的 复杂的。了解FSG和NS的遗传基础很重要：（1）迄今为止的工作一直是主要的 理解肾小球的分子结构的驱动力； （2）遗传诊断影响治疗：有些 突变预测对立体疗法的反应缺乏反应，其他突变预测了对营养补充的反应。 （3）遗传学影响肾移植计划和结果。仍然存在主要差距：（1）大多数FSG/NS案例仍在 通常未解决； （2）疾病的基础很复杂，涉及不同的贡献 跨等位基因频率和渗透率的变体； （3）我们在声明遗传休闲性的能力 单人级别有限； （4）治疗选择有限。那，我们将使用这个大型队列 解决这些差距的新分析方法。我们将在功能上表征许多新等位基因，并且 我们发现的新FSG基因。我们将开发和分发试剂，包括患者衍生的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数据库，并制作 通过Web浏览器获得此数据，以协助研究社区。我们计划：目标1：了解 稀有遗传变异的频谱会导致（或增加）人类FSG和NS的风险。通过利用 大型样本量，我们可以使用否则对疾病基因的功能不足的方法 鉴别。我们将发现与FSG/NS相关的新型基因，以识别高渗透变体 （包括罕见序列变化和拷贝数变体的Burnen测试），定义SNV和 已知FSGS/NS基因中的结构变异，并鉴定与疾病相关的肾小球基因 基因。 AIM 2：定义与疾病相关变体的功能效应。我们将测试效果 基于细胞的测定中的变体/突变，通过突变FSGS/NS基因而开发新的斑马鱼模型，并且 来自FSGS/NS相关突变患者的一组IPS细胞。目标3：我们将聚集在一起 我们所有的基因分型数据，由SNP阵列，WES和WGS生成，以构建和维护公开 可用的变体浏览器，“肾病综合征基因组门户”（NSGP）。 NSGP将包括Alle FSGS/NS的频率数据，功能分类和临床相关。我们将在一个网站上进行总结 - 在我们的FSGS/NS队列中观察到的水平，SNV，插入缺失，结构变体（CNV），并提供质量 报告的变体指标。 NSGP还将有能力接受和合并其他 研究人员和临床遗传学实验室。