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

项目总结