Genomic Data Sharing

基因组数据共享

• 批准号: 10926651
• 负责人: Kathleen Calzone
• 金额: $ 90.29万
• 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/10926651
• 关键词: Address; Administrator; Adopted; Affect; Annual Reports; Authorization documentation; Budgets; CCR; Cell Line; Certification; Clinical Protocols; Clinical Research Protocols; Clinical Trials; Code; Communication; Computer software; Counseling; Data; Development; Disease; Education; Electronic Mail; Elements; Ensure; Funding; Gene Expression; Genome; Genomics; Grant; Human; Informed Consent; Infrastructure; Institution; Intramural Research; Intramural Research Program; Laboratory Scientists; Language; Leadership; Legal; Malignant Neoplasms; Manuals; Metagenomics; Names; Notification; Organism; Participant; Pediatric Oncology Group; Persons; Policies; Procedures; Process; Protocols documentation; Published Comment; Rare Diseases; Recommendation; Research; Research Personnel; Resources; Review Committee; SNP array; Science Policy; Services; Specific qualifier value; System; Testing; Time; Transfer Agreement; United States; United States National Institutes of Health; Update; Writing; data management; data portal; data preservation; data sharing; data sharing networks; data standards; data submission; database of Genotypes and Phenotypes; epigenomics; genome wide association study; genomic data; large scale data; meetings; non-genomic; statistics; timeline; tool; transcriptomics; usability; waiver; web site; working group

This year the NIH Office of Science Policy (OSP) launched the new Data Management and Sharing (DMS) Policy effective January 25, 2023. The DMS Policy mandates sharing of scientific data generated from NIH-funded or conducted research and went into effect 1/25/2023 for laboratory scientists and clinical research protocols going in for Scientific Review. For the Intramural Research Program, a DMS plan is required for scientific data from research associated with a: ZIA (human and non-human research); Clinical protocol that will undergo IC Initial Scientific Review; Genomic Data Sharing (GDS) project The GDS policy applies to all NIH-funded research generating large-scale human or non-human genomic data. Large-scale data including genome-wide association studies (GWAS), single nucleotide polymorphism (SNP) arrays, genome sequence, transcriptomic, metagenomic, epigenomic, and gene expression data. The GDS Policy expanded on November 1, 2018 to include public access to Genomic Summary Results. At that time, the Office of Science Policy (OSP) mandated dbGaP minimal registration for all studies as a means for OSP to communicate with all investigators with policy-applicable studies. OSP has since backed off this mandate, so minimal registrations have been discontinued. Guidance issued from the CCR Director also mandates genomic data sharing for rare diseases/cancers with no minimum thresholds. The Trans-NCI Genomic Data Sharing Working Group adopted the definition of rare disease - a disease that affects less than 200,000 persons in the United States. The DMS Plan incorporates the requirements of both the DMS and GDS policies and addresses six core elements: Data type; Related Tools, Software and/or Code; Data Standards; Data Preservation, Access, and Associated Timelines; Access, Distribution, or Reuse Considerations; and Oversight of Data Management and Sharing. There is also an option to include other elements as applicable. Laboratory scientists completed DMS plans by 1/25/2023 using the Annual Report System. Plans that involved genomics were reviewed by K. Calzone in addition to either Brenda Boersma or Kelly Haskins, with their focus predominately on non-genomic plan elements. Plans were approved, or the investigator was provided with written comments on items to address. DMS plans completed by 1/25/2023 were submitted electronically to OIR in the NIDB. Existing clinical protocols are required to comply at the time of quadrennial review (which CCR does not currently have in place) or as specified by CCR or OIR. New protocols must submit their plan during Scientific Review Committee (SRC). SRC-reviewed plans are revised if applicable, finalized, and approved during Study Initiation. In contrast to the GDS policy, the NCI Office of Data Sharing did not establish a procedure for policy exceptions which can occur because of limitations specified in Tech Transfer agreements. After input from the Office of Science Policy, the NCI Office of Data Sharing, and legal counsel in the Office of Intramural Research, the final determination was that CCR leadership could determine whether to grant a data-sharing waiver. A CCR waiver mechanism has been implemented with the current approver Dr. Misteli or his designee. Investigator Resources Data Sharing Portal: Critical to the infrastructure needed to facilitate investigators is developing and maintaining the CCR Data Sharing Portal (https://service.cancer.gov/gds/). The DMS Policy mandates a DMS Plan (DMSP) and an Institutional Certification (IC) to be completed based on whether the study involves human or non-human organisms or cell lines. DMS plans for new clinical protocols began using the OIR intramural pdf template until the existing Data Sharing portal was modified to create the new DMS plan. Several delays occurred in this process, including a delay in receiving the budget from CBIIT and a delay in CCR rendering a budget decision to move forward. Usability testing was completed by the deadline, and revisions based on the user testing were completed when one CCR leader submitted changes deemed essential. CBIIT had already reallocated Staff to other projects with budget and staffing implications. After an additional delay, the final determination was to launch the portal in its present condition because these items, such as the API for ZIA numbers, CBIIT was not clear that they could even build in the Service Now platform that houses the portal. The permission to launch the portal as is was shared with me on 6/16/2023. However, at that same time, NCI ODS notified us that new Institutional Certification memo templates were established and mandated for use, effective 7/1/2023. CBIIT immediately began that portal revision and investigating how to update each existing Institutional Certification. At the same time, the portal resubmit function was not functioning. As such, CBIIT asked that the launch be delayed until that resubmit fix was made, and the Institutional Certification update was completed. As of July 21, 2023, CBIIT expects to launch the week of August 7, 2023. Brenda Boersma has an email prepared for clinical protocol PI distribution once the launch date is finalized. Support Documents: To support the DMS policy and the new portal, in addition to the CCR Data Management and Sharing Website, we have established the following Standard Operating Procedures (SOPs): 1-RPS 21-Establishing a Data Management Sharing Plan; 2-RPS 22-Requesting a Data Management and Sharing Waiver; 3-RPS 23-Registering a Clinical Trial in dbGaP In addition, the Office of Education and Compliance recommended that instead of integrating portal-specific functionality into the SOPs, those details be put into a Data Management and Sharing Portal User Manual, which could be revised as needed without delays associated with the review/approval process for SOPs. The three SOPs and the Manual are currently on the CCR SOP website. Lastly, we have revised the data sharing WIKI page, renaming it to Data Management and Sharing and reflecting the current Data Sharing landscape and associated resources. Statistics from July 3, 2022-July 4, 2023 Tracking Portal: 565 studies are in the GDS Tracking portal. 26 GDSPs were reviewed, and 23 were approved. 35 ICs were reviewed, and 31 were approved. The GPA Administrator has been auditing the entries for incomplete documents never submitted for review/approval, revisions never resubmitted, and eliminating duplicates. Waivers: One waiver was submitted and approved, IRB001578, ceding data sharing to the Children's Oncology Group. PSO indicates two additional waivers to be submitted: IRB001529-Gulley and IRB01583-Annunziata. Lastly, Dr. Aldape has been notified about the new waiver option as he was considering submitting an Exception. New Study Sensitivity Determinations: GSR Sensitivity Determinations: 52 studies were reviewed, 19 Sensitive, 33 Not Sensitive. Data Sharing: 473 studies are registered in dbGaP, 70 complete registrations, and 403 minimal registrations (discontinued activity). Data was submitted on 19 studies this year and 3 new versions of existing studies. There are 67 studies with some aspect of data submission: 3 additional studies have complete registrations with no data submission. Specifically, 2 are late on submission, and one with no target release date. Lastly, there are 15 studies with data submitted but late on release.

今年，美国国立卫生研究院科学政策办公室（OSP）推出了新的数据管理和共享（DMS）政策，将于2023年1月25日生效。DMS政策要求共享由美国国立卫生研究院资助或开展的研究产生的科学数据，并于2023年1月25日生效，适用于实验室科学家和参加科学审查的临床研究方案。对于校内研究项目，与ZIA（人类和非人类研究）相关的科学数据需要DMS计划；将接受IC初步科学审查的临床方案；基因组数据共享（GDS）项目GDS政策适用于所有nih资助的产生大规模人类或非人类基因组数据的研究。大规模数据包括全基因组关联研究（GWAS）、单核苷酸多态性（SNP）阵列、基因组序列、转录组、宏基因组、表观基因组和基因表达数据。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。当时，科学政策办公室（OSP）要求dbGaP对所有研究进行最低限度的注册，作为OSP与所有研究人员进行政策适用研究沟通的一种手段。OSP后来放弃了这项任务，因此停止了最低限度的登记。CCR主任发布的指南还要求共享罕见病/癌症的基因组数据，没有最低阈值。跨国家癌症研究所基因组数据共享工作组通过了罕见病的定义——一种在美国影响不到20万人的疾病。DMS计划结合了DMS和GDS政策的要求，并解决了六个核心要素：数据类型；相关工具、软件及/或代码；数据标准;数据保存、访问和相关时间表；访问、分发或重用考虑；监督数据管理和共享。还可以选择包括其他适用的元素。实验室科学家使用年度报告系统在2023年1月25日前完成了DMS计划。除了Brenda Boersma或Kelly Haskins之外，K. Calzone还审查了涉及基因组学的计划，他们主要关注非基因组计划元素。计划被批准，或者研究者被提供了书面评论。在2023年1月25日之前完成的DMS计划以电子方式提交给NIDB的OIR。现有的临床方案需要在四年审查时（CCR目前没有）或CCR或OIR指定的情况下遵守。新方案必须在科学审查委员会（SRC）期间提交其计划。如果适用，src审查的计划将在研究启动期间进行修订，最终确定并批准。与GDS政策相反，NCI数据共享办公室没有建立政策例外程序，这些例外可能由于技术转让协议中规定的限制而发生。在听取了科学政策办公室、NCI数据共享办公室和校内研究办公室法律顾问的意见后，最终的决定是由CCR领导层决定是否授予数据共享豁免。CCR豁免机制已由目前的批准人Misteli博士或其指定人员实施。研究者资源数据共享门户：开发和维护CCR数据共享门户（https://service.cancer.gov/gds/）是促进研究者所需的基础设施的关键。DMS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DMS计划（DMSP）和机构认证（IC）。新的临床方案的DMS计划开始使用OIR内部pdf模板，直到修改现有的数据共享门户以创建新的DMS计划。在这个过程中出现了几次延迟，包括从CBIIT接收预算的延迟，以及CCR提交预算决策的延迟。可用性测试在截止日期前完成，当一个CCR负责人提交必要的更改时，基于用户测试的修订完成。工信会已经将工作人员重新分配到其他涉及预算和人员配备的项目。在额外的延迟之后，最终决定以其当前状态启动门户，因为这些项目（例如用于ZIA编号的API）、ciit甚至不清楚它们是否可以在容纳门户的Service Now平台中构建。我在2023年6月16日获得了启动门户的许可。然而，与此同时，NCI ODS通知我们，新的机构认证备忘录模板已经建立并强制使用，自2023年7月1日起生效。ciit立即开始门户修订，并调查如何更新每个现有的机构认证。同时，门户重新提交功能不起作用。因此，ciit要求推迟发布，直到重新提交修复，并完成机构认证更新。截至2023年7月21日，ciit预计将于2023年8月7日推出。Brenda Boersma准备了一封电子邮件，以便在发布日期确定后进行临床协议PI分发。支持文件：为了支持DMS政策和新的门户网站，除了CCR数据管理和共享网站外，我们还制定了以下标准操作程序（sop）： 1-RPS 21-建立数据管理共享计划；2-RPS 22-请求数据管理和共享豁免；此外，教育和合规办公室建议，与其将门户特定的功能集成到标准操作程序中，不如将这些细节纳入数据管理和共享门户用户手册，该手册可以根据需要进行修改，而不会因标准操作程序的审查/批准过程而延迟。这三个SOP和手册目前在CCR SOP网站上。最后，我们修改了数据共享WIKI页面，将其重命名为数据管理和共享，以反映当前的数据共享环境和相关资源。从2022年7月3日至2023年7月4日的统计数据跟踪门户：565项研究在GDS跟踪门户中。审查了26个gdsp，批准了23个。审查了35个ic，批准了31个。GPA管理员一直在审核未提交审阅/批准的不完整文档、未重新提交的修订文档，并消除重复的文档。豁免：一项豁免已提交并批准，IRB001578，将数据共享给儿童肿瘤组。PSO指示提交另外两个豁免：IRB001529-Gulley和IRB01583-Annunziata。最后，aldap博士已被告知新的豁免选项，因为他正在考虑提交例外。新研究敏感性测定：GSR敏感性测定：回顾了52项研究，19项敏感，33项不敏感。数据共享：在dbGaP中注册了473项研究，70项完成注册，403项最小注册（已停止活动）。今年提交了19项研究的数据和3项现有研究的新版本。67项研究有某些方面的数据提交：另外3项研究有完整的注册，没有数据提交。具体来说，有2个提交晚了，还有一个没有目标发布日期。最后，有15项研究提交了数据，但发布较晚。