Genetics and Genomics Core

遗传学和基因组学核心

• 批准号: 10399445
• 负责人: Jonathan Boyd Parr
• 金额: $ 30.62万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10399445
• 关键词: Animals; Bioinformatics; Catalogs; China; Clinical; Collaborations; Collection; Communicable Diseases; Communities; Czech Republic; DNA; Data; Development; Ensure; European; Fostering; Generations; Genetic; Genetic study; Genomics; Genotype; Globus Pallidus; Goals; Human; Hybrids; Immune; Infection; Institution; Laboratories; Malawi; Membrane Proteins; Methods; Minority; Molecular Epidemiology; Monoclonal Antibodies; North Carolina; Order Spirochaetales; Oryctolagus cuniculus; Pathway interactions; Patients; Play; Population Genetics; Process; Reproducibility; Research; Research Personnel; Research Project Grants; Role; Sampling; Scientist; Site; Specimen; Syphilis; Techniques; Training; Treponema pallidum; Universities; Vaccine Antigen; Vaccine Design; Vaccines; Variant; base; bioinformatics pipeline; bioinformatics tool; clinical research site; computerized data processing; cost efficient; data cleaning; data dissemination; data management; deep sequencing; design; experience; genetic analysis; genome sequencing; genomic data; immunogenic; improved; innovation; laboratory facility; next generation sequencing; novel; pathogen; population genetic structure; pre-clinical; public database; sample archive; syphilis vaccine; tool; vaccine candidate; vaccine development; whole genome

ABSTRACT The use of molecular epidemiology and population genetics has revolutionized the ways in which we study infectious diseases and, in particular, pathogen diversity. This revolution has been facilitated by the explosive increase in available genetic data, primarily due to second-generation sequencing. Treponema pallidum subsp. pallidum (TPA) genetic data will play an integral role in the completion of all three CRC Projects. To ensure the quality and robustness of this data across projects, the CRC will support the UNC/Masaryk University Genetics and Genomics Core (GGC). The GGC is a multi-institution core, led by the University of North Carolina, that is designed to enable the CRC to apply state-of-the-art, next-generation sequencing, and bioinformatic tools to catalog the sequence diversity of TPA outer membrane proteins (OMPs). Categorization of this diversity is necessary for developing a broadly protective, globally effective syphilis vaccine using immunogenic OMPs as vaccine antigens. In order to support TPA vaccine development, the GGC will: 1) provide laboratory support for genetic analysis of clinical isolates in order to define the diversity of the TPA “OMPeome”, 2) provide bioinformatic processing and data management for the CRC, including generating cleaned data to all the CRC Projects for analysis and disseminating this data to the scientific community, 3) train CRC investigators in genomic methods and facilitate cross-CRC training, and 4) develop novel tools to advance TPA genomics. The GGC has developed: 1) a detailed plan to ensure efficient collaboration between the core and CRC Projects, 2) processes to ensure the rigor and reproducibility of the data, and 3) plans for the dissemination of data, bioinformatic tools and laboratory methods to the scientific community.

摘要 分子流行病学和人口遗传学的使用已经彻底改变了 我们研究传染病，特别是病原体多样性。这场革命一直是 可用基因数据的爆炸性增长，主要是由于第二代 测序。梅毒螺旋体亚种梅毒(TPA)基因数据将在 完成了所有三个儿童权利中心项目。要确保此数据的质量和健壮性 在项目方面，儿童基金会将支持北卡罗来纳大学/马萨里克大学遗传学和基因组学核心项目 (GGC)。GGC是一个多机构的核心，由北卡罗来纳大学领导，即 旨在使CRC能够应用最先进的下一代测序，以及 生物信息学工具对TPA外膜蛋白(OMP)的序列多样性进行分类。 对这种多样性进行分类是必要的，以发展一种广泛保护、全球有效的 以免疫原性OMPS为疫苗抗原的梅毒疫苗。为了支持TPA疫苗 开发后，GGC将：1)为临床分离株的基因分析提供实验室支持 为了确定TPA的多样性，2)提供生物信息处理和 儿童权利中心的数据管理，包括为所有儿童权利中心项目生成清理后的数据 分析和传播这些数据给科学界，3)培训儿童权利委员会调查人员 基因组方法和促进跨CRC培训，以及4)开发新的工具来促进TPA 基因组学。GGC已经制定了：1)详细的计划，以确保 核心项目和《儿童权利公约》项目，2)确保数据的严格性和可重复性的进程，3) 向科学工作者传播数据、生物信息学工具和实验室方法的计划 社区。