Genomic Data Sharing

基因组数据共享

• 批准号: 10703076
• 负责人: Kathleen Calzone
• 金额: $ 94.76万
• 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/10703076
• 关键词: Address; Administrator; Animal Experimentation; Animal Model; CCR; Cell Line; Certification; Clinical Research; Clinical Trials; Computers; Consent Forms; Data; Data Element; Data Reporting; Databases; Development; Ensure; Environment; Feedback; Funding; Genomics; Human; Human Cell Line; Infectious Agent; Informed Consent; Infrastructure; Intramural Research; Iris; Laboratories; Language; Lead; Learning; Link; Logistics; Maintenance; Malignant Neoplasms; Modification; Monitor; Notification; Online Systems; Organism; Participant; Periodicity; Policies; Policy Compliance; Policy Developments; Positioning Attribute; Process; Protocols documentation; Rare Diseases; Reporting; Research; Research Personnel; Resolution; Resources; Retrieval; Review Committee; Role; Science Policy; Services; Source; Subgroup; Supervision; System; Testing; Time; Training; United States National Institutes of Health; Update; Work; arm; base; dashboard; data integrity; data management; data portal; data sharing; data submission; database of Genotypes and Phenotypes; genomic data; genomic platform; improved; meetings; migration; programs; prospective; repository; response; statistics; timeline; wiki; working group

The NIH Genomic Data Sharing Policy (GDS) applies to NIH-funded research that generates large-scale human or non-human genomic data. The CCR Director mandates genomic data sharing for rare diseases/cancers with no minimum thresholds. The GDS Policy expanded 11/1/2018 to include public access to Genomic Summary Results. The Office of Science Policy (OSP) released the NIH Policy for Data Management and Sharing (DMS Policy) 10/29/2020 that expands scientific data sharing from NIH-funded or conducted research effective 1/25/2023. OSP convened a Clinical Research Subgroup of the Trans NCI DMS Implementation Working Group and Dr. Calzone has been assigned. At the inaugural meeting it was shared that Genomic Program Administrations (GPA) will NOT be involved in DMS policy implementation except through the working group term. GPAs and GPA Administrators will only be involved in GDS content. The Office of Intramural Research (OIR) will lead DMS policy implementation, the intramural Data Management and Sharing Plan template, mechanisms for plan submission, and will monitor for compliance. This subgroup meets monthly until the DMS policy launch. Investigator Resources: Dr. Calzone is the Genomic Program Administrator (GPA) and primary contact for CCR investigators. The GPA Administrator (GPA-A) position was vacant until Margaux Seyler-Schmidt started 2/7/2022. She serves the secondary contact for CCR investigators, the primary contact for CBIIT and assists with data pulls, study registrations and now auditing old and new portal data. Between, 7/6/2021-2/6/2022 all activities were handled by Dr. Calzone. The role of the GPA and GPA-A include attendance at the OSP and ODS periodic meetings to learn about new policy developments that will impact CCR investigators. The GPA works with the GDS regulatory aspects, leads the CCR Sensitivity Review committee with assistance of the GPA A and reviews all entered determinations and discusses with the committee if there are issues. She enters final sensitivity determinations in iRIS in time for scientific review. She serves as the interface when the need arises to engage ODS. She handles any CCR Exception Requests which this year involved one investigator that has not yet moved forward with submission of the exception justification. Lastly, she maintains and updates all the CCR GDS SOPs with the assistance of the GPA-A. The GPA-A serves as lead for logistical, computer, and portal issues. She's been trained and works under GPA'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; maintains the CCR GDS Wiki page, the online GDS key information source for CCR investigators; and enters data into the portal tracking database enabling rapid response to investigator queries about the status of a given project or any possible report requests. Project Summary: 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/gds/. 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) must be maintained in a controlled access environment based on a sensitivity determination. The portal (version 4) launched this year provides the platform for GDS form creation, review, approval, revision if indicated, and retrieval. Version 4 was required because the existing platform, Jira, was no longer going to be supported by NCI so there was a required transition to Service Now with the transition handled by CBIIT. Portal activities this past year included the rebuild of the portal in Service Now which also addressed the following issues: 1-GDSP's and ICs are linked to a project. 2-Improve portal login issues for the GPA and GPA Admin, which greatly reduced the load time. The GDS Tracking Database moved into the existing GDS portal, though the tracking arm is not visible to end users. The portal is organized by project which can be clinical or animal research protocols or laboratory projects of any organism or cell line. Portal projects and documents are established by the investigator or their designee. Despite multiple tests prior the launch of Version 4 there have been several problems including integrity of data migration from Version 3, completed forms not accurately linked to the project, incorrect status reports on form completion, and inconsistency in notifications to the investigator and GPA/GPA Admin that there are documents that require review and sign off. Unfortunately, given the magnitude of the problems, including problems which were CBIIT reportedly fixed but persist, or new problems arising ultimately resulted in us escalating this to the supervisor Larry Brem. This had some limited impact initially but there remain unresolved problems. The GPA and GPA Admin meet weekly with CBIIT representative Jae Song to resolve ongoing issues. Statistics from 7/3/2021-7/4/2021: During data pulls from the new dashboard, we identified additional issues that still require resolution which impact some of the numbers we can report. For example, when the studies were migrated to the new portal, the date the migration occurred became the data the study was created. In addition, form migration from the old to new portal continues as an issue which also impacts data accuracy. So, while we are reporting data below, we plan perform a full audit of all forms/data elements which will begin in 8/2022. Tracking Portal: 514 studies are in the GDS Tracking portal. 39 GDSP's were reviewed and 37 approved. 31 IC's were reviewed 27 approved. No exception requests were submitted in this reporting period however preliminary discussions with Dr. Aldape about submitting an exception but he has not provided the justification. Since version 4 launched mid 3/1022 there have been 12 projects created with 24 GDSPs and 28 ICs. New Studies: GSR Sensitivity Determinations: 63 studies were reviewed, 27 Sensitive, 36 Not Sensitive. Data Sharing: 465 studies are registered in dbGaP, 408 are minimal registrations, 18 in the past year and 57 full registrations, 5 in the past year. Data was submitted on 40 studies, 8 in the past year. Three new versions of existing studies were submitted this year. Lastly there are 14 closed studies without data submission which are awaiting data submission by the PI. With the move to DMS policy when compliance will be overseen by OIR, we will work with these investigators to data share before OIR oversight starts 1/31/2023.

NIH基因组数据共享政策（GDS）适用于NIH资助的产生大规模人类或非人类基因组数据的研究。CCR主任要求共享罕见病/癌症的基因组数据，没有最低门槛。GDS政策于2018年11月1日扩展，包括公众访问基因组摘要结果。科学政策办公室（OSP）于2020年10月29日发布了美国国立卫生研究院数据管理和共享政策（DMS政策），该政策扩大了美国国立卫生研究院资助或开展的研究的科学数据共享，自2023年1月25日起生效。OSP召集了跨NCI DMS实施工作组的临床研究小组，并任命了Calzone博士。在成立大会上，大家一致认为，基因组计划管理部门（GPA）将不参与DMS政策的实施，除非通过工作组任期。GPA和GPA管理员将只参与GDS的内容。校内研究办公室（OIR）将领导DMS政策实施、校内数据管理和共享计划模板、计划提交机制，并监督合规情况。该小组每月开会一次，直到DMS策略启动。研究者资源：Calzone博士是基因组项目管理员（GPA）和CCR研究者的主要联系人。GPA管理员（GPA- a）的职位空缺，直到Margaux seller - schmidt于2022年7月2日上任。她是CCR调查员的第二联系人，也是CBIIT的主要联系人，并协助数据提取，研究注册以及现在审计新旧门户数据。在2021年7月6日至2022年2月6日期间，所有活动都由Calzone博士处理。GPA和GPA- a的作用包括参加OSP和ODS的定期会议，以了解将影响CCR调查员的新政策发展。GPA与GDS监管方面合作，在GPA A的协助下领导CCR敏感性审查委员会，审查所有提交的决定，并与委员会讨论是否存在问题。她及时在iRIS中进行最后的灵敏度测定，以便进行科学审查。她是联络混乱办的联络人。她处理今年涉及一名尚未提交例外理由的调查人员的任何CCR例外请求。最后，她在GPA-A的协助下维护和更新所有CCR GDS sop。GPA-A负责后勤、计算机和门户问题。她接受过培训，并在GPA的监督下工作：在门户网站上完成GDSP和IC提交的初步审核，如果需要修改，及时反馈给研究者，并进入dbGaP研究注册，支持研究者进行数据共享；将研究输入基因组汇总结果在线系统，供CCR敏感性审查委员会审查；维护CCR GDS Wiki页面，这是CCR调查人员的在线GDS关键信息源；并将数据输入门户跟踪数据库，以便快速响应调查人员对给定项目状态或任何可能的报告请求的查询。项目概述：基因组数据共享基础设施：促进研究者基因组数据共享（GDS）所需的基础设施的关键是CCR GDS门户https://service.cancer.gov/gds/的开发和维护。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，完成基因组数据共享计划（GDSP）和/或机构认证（IC）。GDSP文档数据类型、提交库、建议提交和发布时间表。人类（包括人类细胞系）模式生物、非人类细胞系和感染性生物都需要这种形式。IC文件同意数据共享、数据使用限制以及是否必须在基于敏感性确定的受控访问环境中维护基因组摘要结果（GSR）。今年推出的门户（版本4）为GDS表单的创建、审查、批准、修改（如果需要的话）和检索提供了平台。版本4是必需的，因为现有的平台Jira将不再受NCI的支持，因此必须过渡到Service Now，并由CBIIT处理过渡。过去一年的门户活动包括在Service Now中重建门户，这也解决了以下问题：1-GDSP和ic与一个项目相关联。改善了GPA和GPA Admin的门户登录问题，大大减少了加载时间。GDS跟踪数据库移动到现有的GDS门户，尽管跟踪臂对最终用户不可见。门户是由项目组织的，可以是临床或动物研究协议或任何生物体或细胞系的实验室项目。门户项目和文件由调查人员或其指定人员建立。尽管在版本4发布之前进行了多次测试，但仍然存在一些问题，包括从版本3迁移的数据完整性、完成的表单没有准确地链接到项目、表单完成的状态报告不正确，以及通知调查员和GPA/GPA管理员有文档需要审查和签署的不一致。不幸的是，考虑到问题的严重性，包括那些据称已经解决但仍然存在的问题，或者新出现的问题，最终导致我们将此事升级到主管拉里·布雷姆（Larry Brem）。这在最初产生了一些有限的影响，但仍有一些问题尚未解决。GPA和GPA管理人员每周与ciit代表Jae Song会面，以解决持续存在的问题。2021年7月3日至2021年7月4日的统计数据：在从新仪表板提取数据的过程中，我们发现了一些仍然需要解决的问题，这些问题会影响我们可以报告的一些数字。例如，当将研究迁移到新的门户时，迁移发生的日期将成为创建研究的数据。此外，从旧门户到新门户的表单迁移仍然是一个影响数据准确性的问题。因此，当我们在下面报告数据时，我们计划从2022年8月开始对所有表单/数据元素进行全面审计。跟踪门户：GDS跟踪门户中有514项研究。审核了39个GDSP，批准了37个。审核了31个IC，批准了27个。在本报告所述期间没有提交例外请求，但与aldap博士就提交例外进行了初步讨论，但他没有提供理由。自版本4于1922年3月中旬发布以来，已经创建了12个项目，包含24个gdsp和28个ic。新研究：GSR敏感性测定：回顾了63项研究，27项敏感，36项不敏感。数据共享：465项研究在dbGaP中注册，408项是最小注册，18项是过去一年注册的，57项是过去一年注册的，5项是过去一年注册的。提交了40项研究的数据，其中8项是去年提交的。今年提交了现有研究的三个新版本。最后，还有14项未提交数据的封闭研究正在等待PI提交数据。随着转向DMS政策，合规将由OIR监督，我们将与这些调查人员合作，在OIR监督开始之前共享数据。