Genetics and Genomics Core

遗传学和基因组学核心

• 批准号: 9923553
• 负责人: Jonathan Boyd Parr
• 金额: $ 29.55万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9923553
• 关键词: Animals; Archives; Bioinformatics; Catalogs; China; Clinical; Collaborations; Collection; Communicable Diseases; Communities; Czech Republic; DNA; Data; Databases; 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; 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 分子流行病学和群体遗传学的应用彻底改变了 我们研究传染病，特别是病原体的多样性。这场革命 主要由于第二代基因数据的爆炸性增加，这为可用基因数据的爆炸性增加提供了便利 测序梅毒螺旋体梅毒（TPA）基因数据将在以下方面发挥不可或缺的作用： 完成所有三个CRC项目。为了确保这些数据的质量和稳健性， 项目，CRC将支持生物技术研究所/马萨里克大学遗传学和基因组学核心 （GGC）。GGC是一个多机构核心，由北卡罗来纳州大学领导， 旨在使CRC能够应用最先进的下一代测序技术， 利用生物信息学工具对TPA外膜蛋白（OMP）的序列多样性进行分类。 这种多样性的分类是必要的，以制定一个广泛的保护，全球有效的， 使用免疫原性OMP作为疫苗抗原的梅毒疫苗。为了支持TPA疫苗 GGC将：1）为临床分离株的遗传分析提供实验室支持 为了定义TPA“OMPeome”的多样性，2）提供生物信息学处理， CRC的数据管理，包括为所有CRC项目生成清理数据， 分析并向科学界传播这些数据，3）培训CRC调查人员， 基因组方法和促进交叉CRC培训，以及4）开发新的工具来推进TPA 基因组学GGC制定了：1）详细的计划，以确保 核心和CRC项目，2）确保数据的严谨性和可重复性的流程，以及3） 向科学界传播数据、生物信息学工具和实验室方法的计划 社区