Genomic Data Sharing

基因组数据共享

• 批准号: 10487267
• 负责人: Kathleen Calzone
• 金额: $ 152.95万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 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/10487267
• 关键词: Address; Administrator; Adopted; Affect; Animal Experimentation; Animal Model; Annual Reports; CCR; Cell Line; Certification; Clinical Protocols; Clinical Research; Computers; Consent Forms; Data; Databases; Development; Disease; Education; Ensure; Environment; Feedback; Funding; Gene Expression; Genome; Genomics; Human; Human Cell Line; Infectious Agent; Informed Consent; Infrastructure; Iris; Laboratories; Language; Lead; Learning; Logistics; Maintenance; Malignant Neoplasms; Metagenomics; Modification; Molecular; Nursing Research; Online Systems; Organism; Participant; Pathology; Periodicity; Persons; Policies; Policy Developments; Positioning Attribute; Process; Protocols documentation; Rare Diseases; Reporting; Research; Research Personnel; Resources; Retrieval; Review Committee; Role; SNP array; Science Policy; Series; Services; Source; Supervision; System; Testing; Time; TimeLine; Training; United States; United States Food and Drug Administration; United States National Institutes of Health; Update; Work; arm; base; data portal; data sharing; data submission; database of Genotypes and Phenotypes; epigenomics; genome wide association study; genomic data; genomic platform; improved; large scale data; meetings; phenotypic data; programs; prospective; rare cancer; repository; response; statistics; transcriptomics; usability; wiki; working group

Genomic Data Sharing Infrastructure: Critical to the infrastructure needed to facilitate investigator Genomic Data Sharing (GDS) is the development and maintenance of CCR GDS Portal https://service.cancer.gov/ccrgds/. The GDS Policy mandates prospectively a Genomic Data Sharing Plan (GDSP) and/or an Institutional Certification (IC) be completed based on whether the study involves human or non-human organisms or cell lines. The GDSP documents data type(s), repository for submission, and proposed submission and release timeline. This form is required of human (including human cell lines) model organisms, non-human cell lines, and infectious organisms. The IC) documents consent for data sharing, data use limitations and whether Genomic Summary Results (GSR) need to be maintained in a controlled access environment based on a sensitivity determination. The portal version 2 provides the platform for GDS form creation, review, approval, revision if indicated, and retrieval. The portal is organized by project which can be clinical or animal research protocol or laboratory project of any organism or cell line. Portal projects and documents can be established by the investigator or their designee. In the case of clinical protocols, this most often is Protocol Support Office staff but can also include others such as research nurses and laboratory investigators. Activities associated with the portal this past year have included enhancements to the portal (version 3) addressing the following issues: 1-GDSP's originally generated and approved in portal version 1 have been stored unattached to a project in the version 2 portal. This required establishing projects that correspond to each GDSP with project specific team access based on the original submission. 2-Improve portal login issues. For the GPA and GPA Admin, the portal was taking greater than 5 minutes to load. This is not an issue for end users entering forms, but an issue for those with access to all projects. The system remains slow for the GPA and GPA Admin but is improved. 3-Create a tracking database arm to the portal as the program JIRA was no longer going to be supported by NCI, a program which served as the original tracking database. The tracking arm to the portal has been created including a report function, underwent usability testing, all existing data uploaded into the system and audited for accuracy. Statistics from 7/9/2020-7/8/2021: Tracking Portal: A total of 505 studies reside in the new GDS Tracking portal, 86 in this reporting period. There were 40 GDSP's reviewed and 46 IC's reviewed and one exception request submitted in this reporting period. New Studies: 77 new studies identified from either iRIS (n=61) or annual reports (n=16). Genomic Summary Results Sensitivity Determinations: 61 studies were reviewed for a Genomic Sensitivity Determination, of which 18 were Sensitive and 43 Not Sensitive. dbGaP registrations: 439 studies are registered, 105 in this reporting period. Of those 71 were minimal registration. Two studies were deleted from dbGaP. Data Sharing: A total of 10 studies completed data submission and the data were released. There were also 8 studies that have data submission in process consisting of: 1 waiting on molecular data and sequencing data; 1 waiting on molecular data; 1 waiting on sequencing data; and 8 waiting on phenotype data. 14 studies closed without data sharing. Investigator Resources: Dr. Calzone serves as CCR Genomic Program Administrator (GPA) and is the primary contact for CCR investigators. The GPA Administrator (GPA-A) Logan Manlove departed his position on July 6, 2021 and this position is posted. In the interim all activities are being handled by Dr. Calzone. All dbGaP registrations performed by Mr. Manlove have been re-assigned to Dr. Calzone. The role of the GPA and GPA-A include attendance at the NIH Office of Science Policy Data Sharing and the NCI Office of Data Sharing periodic meetings to learn about new policy developments that will impact CCR investigators. The GPA, Dr. Calzone works with the GDS regulatory aspects which included developing and presenting a GDS training session for NIH Intramural investigators on 12/1/2020 as part of the OHSRP Education Series. Dr. Calzone leads the CCR Sensitivity Review committee and reviews all entered determinations and discusses with the committee if there are issues. She enters all final sensitivity determinations in iRIS in time for scientific review. Dr. Calzone serves as the interface when the need arises to engage the NCI Office of Data Sharing. She also handles any CCR Exception Request which this year involved investigators in the Laboratory of Pathology, a request in the final stage of approval. Lastly, she maintains and updates all the CCR GDS SOPs. The GPA-A serves as the lead for logistical, computer, and portal issues. Once hired, the GPA-A replacement will be trained and work under Dr. Calzone's supervision to: complete the initial reviews of GDSP and IC submissions in the portal, provide timely feedback to investigators if modifications are required, and enter dbGaP study registrations and supports investigators in the data sharing process; enter studies into the Genomic Summary Result online system for review by the CCR Sensitivity Review committee; maintain the CCR GDS Wiki page, the online GDS key information source for CCR investigators; and enter data into the portal tracking database enabling rapid response to investigator queries about the status of a given project or any possible report requests.

基因组数据共享基础设施：开发和维护CCR GDS门户网站https://service.cancer.gov/ccrgds/对于促进研究者基因组数据共享（GDS）所需的基础设施至关重要。GDS政策要求根据研究是否涉及人类或非人类生物体或细胞系，前瞻性地完成基因组数据共享计划（GDSP）和/或机构认证（IC）。GDSP记录数据类型、提交的存储库以及建议的提交和发布时间轴。人（包括人细胞系）模型生物、非人细胞系和感染性生物均需要该表。IC记录了数据共享同意、数据使用限制以及是否需要根据敏感性确定在受控访问环境中维护基因组总结结果（GSR）。门户版本2为GDS表单的创建、审查、批准、修订（如果需要）和检索提供了平台。该门户网站按项目组织，可以是任何生物体或细胞系的临床或动物研究方案或实验室项目。门户项目和文件可由研究者或其指定人员建立。在临床协议的情况下，这通常是协议支持办公室的工作人员，但也可以包括其他人，如研究护士和实验室调查员。过去一年与门户相关的活动包括对门户（第3版）的增强，以解决以下问题：1-最初在门户第1版中生成和批准的GDSP已单独存储在第2版门户中的项目中。这需要建立与每个GDSP相对应的项目，并根据原始提交的项目特定团队访问权限。2-改善门户登录问题。对于GPA和GPA管理员，门户加载时间超过5分钟。这不是最终用户输入表单的问题，而是那些可以访问所有项目的用户的问题。GPA和GPA管理员的系统仍然很慢，但已经得到改进。3-创建一个跟踪数据库手臂的门户网站，因为程序JIRA将不再支持NCI，一个程序，作为原来的跟踪数据库。门户网站的跟踪功能已经创建，包括报告功能，经过可用性测试，所有现有数据都上传到系统，并对其准确性进行了审计。2020年7月9日至2021年7月8日的统计数据：跟踪门户网站：新的GDS跟踪门户网站上共有505项研究，其中86项在本报告期内。在本报告所述期间，审查了40份GDSP，审查了46份IC，并提交了一份例外申请。新研究：从iRIS（n=61）或年度报告（n=16）中识别出77项新研究。基因组敏感性测定：对61项研究进行了基因组敏感性测定，其中18项敏感，43项不敏感。dbGaP登记：登记了439项研究，其中105项在本报告期内。其中71人是最低限度的登记。从dbGaP中删除了两项研究。数据共享：共有10项研究完成数据提交并发布。还有8项研究正在进行数据提交，包括：1项等待分子数据和测序数据; 1项等待分子数据; 1项等待测序数据; 8项等待表型数据。14项研究在未共享数据的情况下关闭。研究者资源：Calzone博士担任CCR基因组计划管理员（GPA），是CCR研究者的主要联系人。GPA管理员（GPA-A）Logan Manlove于2021年7月6日离职，该职位已发布。在此期间，所有活动都由Calzone博士负责。由Manlove先生执行的所有dbGaP配准已重新分配给Calzone博士。GPA和GPA-A的作用包括出席NIH科学政策数据共享办公室和NCI数据共享办公室定期会议，以了解将影响CCR研究人员的新政策发展。Calzone与GDS监管方面合作，其中包括在12/1/2020为NIH校内研究人员开发和举办GDS培训课程，作为OHSRP教育系列的一部分。Calzone博士领导CCR敏感性审查委员会，审查所有输入的决定，并与委员会讨论是否存在问题。她及时将所有最终灵敏度测定结果输入iRIS，以便进行科学审查。当需要与NCI数据共享办公室合作时，Calzone博士担任界面。她还处理任何CCR例外请求，今年涉及病理学实验室的研究人员，这是一个处于最后批准阶段的请求。最后，她维护和更新所有CCR GDS SOP。GPA-A是物流、计算机和门户问题的领导者。一旦被聘用，GPA-A的替代者将接受培训，并在Calzone博士的监督下工作：完成门户网站中GDSP和IC提交的初步审查，如果需要修改，及时向研究者提供反馈，并在数据共享过程中输入dbGaP研究注册和支持研究者;将研究输入基因组总结结果在线系统，供CCR敏感性审查委员会审查;维护CCR GDS Wiki页面（CCR研究者的在线GDS关键信息源）;将数据输入门户跟踪数据库，以便快速响应研究者关于特定项目状态的查询或任何可能的报告请求。