Data Analysis Center for Somatic Mosaicism Across Human Tissues Network

人体组织网络体细胞镶嵌数据分析中心

• 批准号: 10662721
• 负责人: Peter J Park
• 金额: $ 200万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2028-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10662721
• 关键词: Benchmarking; Bioinformatics; Biological Assay; Biological Process; Catalogs; Cell Fraction; ClinVar; Cloud Computing; Communities; Complex; Computer software; Computing Methodologies; Consult; Controlled Environment; Copy Number Polymorphism; DNA Insertion Elements; DNA Sequence Rearrangement; DNA Transposable Elements; Data; Data Analyses; Data Collection; Data Set; Databases; Detection; Development; Diploidy; Disease; Ensure; Environment; Funding; Genome; Genomics; Goals; Haplotypes; Health; Image; Individual; Ingestion; International; Intuition; Knowledge; Lead; Malignant Neoplasms; Measures; Metadata; Methods; Microsatellite Repeats; Mosaicism; Mutation; Population Heterogeneity; Positioning Attribute; Process; Protocols documentation; Quality Control; Regulation; Reproducibility; Research Personnel; Resources; Role; Sampling; Scheme; Scientist; Secure; Single Nucleotide Polymorphism; Software Engineering; Standardization; Technology; Testing; Tissue Procurements; Tissues; United States National Institutes of Health; Variant; Visual; Visualization; Visualization software; Work; archive data; bioinformatics tool; cloud platform; cohort; computational pipelines; data access; data analysis pipeline; data and analysis portal; data ecosystem; data management; data modeling; data portal; data sharing; data standards; data submission; data visualization; design; detection method; experience; flexibility; genome-wide; human tissue; improved; insertion/deletion mutation; large scale data; member; metadata standards; mosaic variant; novel strategies; single cell technology; tool; user-friendly; variant detection; web services

PROJECT SUMMARY The goal of the Somatic Mosaicism across Human Tissues (SMaHT) Network is to better characterize the occurrence of mosaic variants in human tissues and to understand their role in the regulation of biological processes that impact health and disease. The SMaHT Data Analysis Center (DAC) aims to collect and curate all data generated in the Network; assess, develop, and apply state-of-the-art analytical pipelines; and produce a variant catalog and a data portal for the scientific community. We have assembled a team of investigators, bioinformatics scientists, data curators, and software developers with a strong track record in mosaic variant analysis, long-read data analysis, data portal development, visualization, large-scale data management and computing, and development of secure and flexible cloud technologies. In Aim 1, we will work with the Network members to define data and metadata standards and ensure that high-quality data are generated, processed, and annotated uniformly and efficiently. In Aim 2, we will perform benchmark studies for the current tools and technologies for identification of mosaic variants and lead an effort to define and implement analytical pipelines on a cloud platform. We will also develop new approaches as needed. We will ensure that a comprehensive set of mosaic variants of all types (single nucleotide variants, indels, copy number variants, translocations, complex rearrangements, transposable element insertions, microsatellite mutations, repeat expansions, etc.) are identified, using short- and long-read platforms, genome-wide and targeted assays, and bulk and single cell technologies. In Aim 3, we will build a user-friendly and interactive data portal containing a variant catalog and featuring a read-level variant browser to enable the scientific community to fully utilize the Network data. We will ensure that all methods and processes are documented for full reproducibility and that all tools and data are freely available to the community. 1

项目摘要 跨人类组织的体细胞嵌合体（SMaHT）网络的目标是更好地表征 嵌合体变体的研究，并了解它们在调节生物过程中的作用， 影响健康和疾病。SMaHT数据分析中心（DAC）旨在收集和管理所有生成的数据 在网络中;评估，开发和应用最先进的分析管道;并产生一个变量目录， 科学界的数据门户。我们组建了一个由生物信息科学家， 数据管理员和软件开发人员，在马赛克变体分析、长时间读取数据方面有着良好的记录 分析、数据门户开发、可视化、大规模数据管理和计算以及开发 安全和灵活的云技术。在目标1中，我们将与网络成员合作定义数据， 元数据标准，确保高质量的数据得到统一的生成、处理和注释， 有效地。在目标2中，我们将对现有的识别工具和技术进行基准研究 mosaic变体，并领导在云平台上定义和实施分析管道的工作。我们将 还根据需要开发新方法。我们将确保一套全面的马赛克变种的所有类型 （单核苷酸变异，插入缺失，拷贝数变异，易位，复杂重排，转座） 元件插入、微卫星突变、重复扩增等）艾德，使用短读和长读 平台、全基因组和靶向测定以及批量和单细胞技术。在目标3中，我们将建立一个 用户友好的交互式数据门户，包含变量目录，并具有读取级变量浏览器， 使科学界能够充分利用网络数据。我们将确保所有方法和流程 所有的工具和数据都是免费提供给社区的。 1