Data Management and Analysis Core

数据管理与分析核心

• 批准号: 10419456
• 负责人: Bjoern Peters
• 金额: $ 17.33万
• 依托单位: LA JOLLA INSTITUTE FOR IMMUNOLOGY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-15 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10419456
• 关键词: Award; Back; Blood Donations; Cells; Clinical; Collaborations; Communities; Computer software; Cytometry; Data; Data Analyses; Data Coordinating Center; Data Element; Data Management Resources; Data Set; Database and Analysis Portal; Databases; Enrollment; Ensure; Funding; Gene Expression; Genomics; Goals; Guidelines; High-Throughput Nucleotide Sequencing; Immune response; Immunology; Infection; Internet; Longitudinal Studies; Manuals; Metadata; Methods; National Institute of Allergy and Infectious Disease; Patients; Policies; Population; Procedures; Process; Quality Control; Recommendation; Reporting; Reproducibility; Research Project Grants; Sampling; Services; Standardization; Statistical Data Interpretation; System; T cell receptor repertoire sequencing; T-Lymphocyte; Target Populations; Time; United States National Institutes of Health; Update; Vaccination; Work; analysis pipeline; automated analysis; base; central database; cohort; complex data; computerized data processing; data analysis pipeline; data management; data sharing; data standards; data submission; differential expression; experience; experimental study; high dimensionality; human subject; human subject protection; improved functioning; instrument; interest; large datasets; large scale data; multidimensional data; programs; public repository; reference genome; repository; respiratory pathogen; single-cell RNA sequencing; success; transcriptome sequencing; transcriptomics; user-friendly

Project Summary The Data Management and Analysis Core (DMAC) will continue to provide centralized data management and analysis services for the LJI HIPC center projects and cores, as it has successfully done since the inception of the HIPC Program at LJI in 2015. Further, the DMAC will ensure the ongoing timely submission of data and data analyses obtained under this award to the ImmPort database and other repositories identified by NIAID. For centralized data management, we will utilize our in-house, data management system of interconnected databases and analysis scripts. This is centered around the Donor Record Administration System (DoRAS) for tracking donors and samples along with clinical information. Here we will extend DoRAS to ensure that all clinical information relevant to the present proposal can be captured. The database will be accessible through the internet and provide a consistent basis to select samples and interpret results. All information in DoRAS is de-identified, so that research projects will not have access to sensitive information, allowing data to be freely shared. In terms of data analysis services, the DMAC will build on the procedures established successfully in the last 6 years and provide a set of automated analysis pipelines that take data generated in each Project and provide standardized analyses that will facilitate inter-project comparisons and reproducibility. Pipelines for bulk RNA-seq have already been fully implemented including user friendly web reports for the generated results. Initial pipelines for single-cell- RNA-seq analysis have been established, and will continue to be optimized. For high-dimensional cytometry analysis as generated by flow or mass-cytometry, we will be using a combination of traditional manual gating approaches and directed automated gating methods, in particularly Directed Automated Filtering and Identification of cell populations (DAFI)1, which was developed in the previous funding period. Also, we will optimize and automate a TCR-seq analysis pipeline that will identify TCRs in various experimental settings. Power calculations will also be provided. To facilitate efficient data sharing with ImmPort, and to follow guidelines for data standards set by the newly introduced HIPC Coordinating Center (HCC), we will take advantage of the fact that the data generated through automated pipelines in this proposal is already in a standardized format, and ties back to the sample and human subject information captured in DoRAS. Updates to data standards are easily implemented in these pipelines, and will generate the desired export format for ImmPort, GEO or SRA. Additionally, DMAC will provide dedicated staff with experience in data submissions to ensure that study specific data elements not covered by the automated pipelines will be appropriately submitted. We have extensive experience and success with this approach, as evidenced by our track record of submissions in the last funding period.

项目概要 数据管理和分析核心（DMAC）将继续提供集中数据管理 为 LJI HIPC 中心项目和核心提供分析服务，正如它自成立以来所成功完成的那样 2015 年 LJI 的重债穷国计划。此外，DMAC 将确保持续及时提交数据和 根据该奖项对 ImmPort 数据库和 NIAID 确定的其他存储库进行的数据分析。 对于集中数据管理，我们将利用我们的内部数据管理系统 互连的数据库和分析脚本。这以捐赠者记录管理系统为中心 (DoRAS) 用于跟踪捐赠者和样本以及临床信息。这里我们将扩展DoRAS来保证 可以捕获与本提案相关的所有临床信息。数据库将可访问 通过互联网，为选择样本和解释结果提供一致的基础。所有信息在 DoRAS 是去标识化的，因此研究项目将无法访问敏感信息，从而允许数据 可以自由分享。 在数据分析服务方面，DMAC 将建立在 DMAC 成功建立的程序的基础上。 过去 6 年的数据，并提供一组自动分析管道，获取每个项目中生成的数据并 提供标准化分析，以促进项目间比较和可重复性。散装管道 RNA-seq 已经全面实施，包括生成结果的用户友好的网络报告。 单细胞 RNA-seq 分析的初步流程已经建立，并将继续优化。为了 通过流式或质谱流式细胞术生成的高维细胞术分析，我们将使用组合 传统的手动门控方法和定向自动门控方法，特别是定向 细胞群自动过滤和识别 (DAFI)1，是在之前的资助中开发的 时期。此外，我们将优化和自动化 TCR-seq 分析流程，该流程将识别各种类型的 TCR 实验设置。还将提供功率计算。 促进与 ImmPort 的高效数据共享，并遵循 ImmPort 制定的数据标准指南 新推出的重债穷国协调中心（HCC），我们将利用生成的数据这一事实 该提案中的通过自动化管道已经采用标准化格式，并且与示例联系在一起 以及 DoRAS 中捕获的人类受试者信息。数据标准的更新很容易在这些中实现 管道，并将生成 ImmPort、GEO 或 SRA 所需的导出格式。此外，DMAC 将提供 具有数据提交经验的专门工作人员，以确保研究未涵盖的特定数据元素 自动化管道将适当提交。我们在这方面拥有丰富的经验和成功的经验 方法，正如我们在上一个资助期间提交的记录所证明的那样。