Core B - Technical Services

核心 B - 技术服务

• 批准号: 10463548
• 负责人: MICHAEL E TALKOWSKI
• 金额: $ 61.99万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-10 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10463548
• 关键词: 3-Dimensional; Alleles; Bayesian Modeling; Biological Assay; Catalogs; Categories; Cell Line; Cell model; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Collection; Communities; Complex; Copy Number Polymorphism; Data; Data Analyses; Data Set; Databases; Disease; Engineering; Family; Female; Fertilization; Foundations; GNRH1 gene; Gene Expression Profile; Gene Expression Profiling; General Hospitals; Genes; Genome; Genomic medicine; Genomics; Human; Idiopathic Hypogonadotropic Hypogonadism; Individual; Infertility; Joints; Kallmann Syndrome; Massachusetts; Methods; Modeling; Molecular; Mutation; Neurodevelopmental Disorder; Neurons; Pathogenicity; Pathway interactions; Patients; Phenotype; Point Mutation; Population; Process; Reagent; Reproductive Medicine; Research; Resources; Risk; Sampling; Scoring Method; Series; Services; System; Technology; Untranslated RNA; Variant; biobank; case control; cloud based; cohort; computerized data processing; computerized tools; de novo mutation; dosage; exome; exome sequencing; follow-up; functional genomics; gene discovery; genetic architecture; genome sequencing; genomic data; genomic variation; human disease; induced pluripotent stem cell; insertion/deletion mutation; insight; loss of function; loss of function mutation; male; multidisciplinary; novel; prime editing; progenitor; programs; rare variant; trait; transcriptome; transcriptome sequencing; transmission process; variant detection; whole genome

PROJECT ABSTRACT The Center for Reproductive Medicine (CRM) represents a multi-disciplinary program to explore the genetic architecture of infertility. The CRM Genomics Core (GC) described herein envisages providing a centralized and catalytic resource for genomic variation, statistical association, and functional perturbations for all components of this overarching CRM program. This genomics hub will specifically catalyze discoveries by providing expertise in the data and methods that will be leveraged for deeper insights into rare and common forms of infertility in Projects 1 and 2, respectively. The GC will also serve as the focal point for cross-fertilization of data, analyses, and functional modeling across the program. Over the last several years, we have developed a compendium of computational tools, statistical approaches, and functional genomics methods to interrogate the mutational spectrum of variation in human diseases. Our methods incorporate joint analyses of short variants (SNVs, indels) and structural variants (SVs), including canonical balanced SVs and copy number variants (CNVs), as well as a diverse catalog of complex SVs that are surprisingly abundant and associated with an array of human disease. These studies have required methods to uniformly generate, process, and rigorously analyze genomics datasets for association studies. In the GC, we will discover and annotate variation, interpret association against population-scale datasets in excess of 1,000,000 genomes from our related studies, and perform scalable engineering to generate an allelic series of perturbations in genes associated with rare and common forms of infertility using human induced pluripotent stem cell (hiPSC) derived GnRH models. Overall, we will support the CRM by completing three objectives related to providing datasets, methods, and functional resources. Objective 1 will develop a comprehensive genomics resource from exome, genome and long-read sequencing, and uniform data processing of the CRM cohorts. Objective 2 will perform integrated rare variant association and interpretation of these datasets by jointly analyzing CRM cohorts with population-scale datasets generated in our genome aggregation database (gnomAD) project and complex disease consortia studies. Objective 3 will then perform scalable CRISPR perturbation of infertility genes in GnRH neuronal models by engineering loss-of-function mutations and an allelic series for select infertility genes. Transcriptional profiling in the genomics core will identify signatures associated with perturbation of these infertility genes, and will seek convergence of these signatures on a small number of infertility relevant pathways. All CRISPR-engineered models will be distributed relevant projects for further functional assays, and all data and models will be made openly available for distribution to the community. These objectives in the genomics hub of the CRM will thus provide datasets, gene discoveries, and CRISPR-engineered isogenic models to facilitate new insights into infertility within the CRM and the broader research community.

项目摘要 生殖医学中心 (CRM) 是一个探索遗传因素的多学科项目。 不孕不育的建筑。本文描述的 CRM Genomics Core (GC) 设想提供一个集中的、 基因组变异、统计关联和所有组件的功能扰动的催化资源 这个总体 CRM 计划的一部分。该基因组学中心将通过提供专业知识来专门促进发现 数据和方法将用于更深入地了解罕见和常见的不孕症形式 分别为项目 1 和 2。 GC 还将作为数据、分析、 以及整个程序的功能建模。在过去的几年里，我们编制了一份纲要 计算工具、统计方法和功能基因组学方法来询问突变 人类疾病的变异谱。我们的方法结合了短变异（SNV、插入缺失）的联合分析 和结构变异 (SV)，包括规范平衡 SV 和拷贝数变异 (CNV)，以及 复杂的 SV 种类繁多，数量惊人，并且与一系列人类疾病相关。 这些研究需要统一生成、处理和严格分析基因组数据集的方法 用于关联研究。在 GC 中，我们将发现并注释变异，解释关联 来自我们相关研究的超过 1,000,000 个基因组的人口规模数据集，并执行可扩展的操作 工程在与罕见和常见形式相关的基因中产生一系列等位基因扰动 使用人类诱导多能干细胞 (hiPSC) 衍生的 GnRH 模型治疗不孕症。总体而言，我们将支持 CRM 通过完成与提供数据集、方法和功能资源相关的三个目标。 目标 1 将开发外显子组、基因组和长读长的综合基因组学资源 CRM 队列的排序和统一数据处理。目标2将执行集成的稀有变体 通过联合分析 CRM 队列和人口规模来关联和解释这些数据集 我们的基因组聚合数据库 (gnomAD) 项目和复杂疾病联盟生成的数据集 研究。 Objective 3 随后将对 GnRH 神经元中的不孕基因进行可扩展的 CRISPR 扰动 通过设计功能丧失突变和选定不孕基因的等位基因系列来建立模型。 基因组学核心中的转录分析将识别与这些干扰相关的特征 不孕基因，并将寻求这些特征在少数不孕相关途径上的收敛。 所有 CRISPR 工程模型将分发相关项目以进行进一步的功能测定，并且所有数据 模型将公开分发给社区。基因组学的这些目标 因此，CRM 中心将提供数据集、基因发现和 CRISPR 工程等基因模型 促进 CRM 和更广泛的研究界对不孕不育症的新见解。