Genomic Data Sharing

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/ccrgds/的开发和维护。根据研究是否涉及人类或非人类生物体或细胞系，GDS政策可能要求提供以下文件。基因组数据共享计划（GDSP）表单记录了数据类型、提交存储库、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。机构认证（IC）文件同意数据共享、数据使用限制以及是否需要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）。门户版本2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。门户是按项目组织的，可以是临床或动物研究方案，也可以是任何生物体或细胞系的实验室项目。门户项目和文件可以由调查员或其指定人员建立。就临床方案而言，这通常是方案支持办公室的工作人员，但也可以包括其他人员，如研究护士和实验室调查员。去年与门户网站有关的活动包括：1 .维护和更新用户组2 .通过门户网站发送的ic备忘录有时无法生成提交内容的副本。在发送到中间服务器以生成最终IC PDF之前，将保存提交包的副本。如果PDF生成失败，我们将为团队重新生成IC数据包，但研究者有时必须多次签署相同的IC。这个问题花了好几周的时间来确定问题的根源并加以解决。从2020年7月开始，中国国际贸促会启动了进一步提升门户的工作。我们目前每周召开一次会议，讨论以下事项：1- gdsp最初在门户版本1中生成和批准，已单独存储在版本2门户的项目中。第一个优先级是建立与每个GDSP相对应的项目，并基于原始提交的项目特定团队访问。解决门户登录问题。对于GPA和GPA Admin，门户的加载时间可能超过5分钟或更长。对于输入表单的最终用户来说，这不是一个问题，但是对于那些可以访问所有项目的用户来说，这是一个问题。3 .将JIRA跟踪数据库合并到portal中。目前，JIRA是用于跟踪GDS项目状态和生成报告的平台。但是，这会导致类似的数据存储在两个位置。考虑到门户登录问题和门户中有限的搜索功能，所有已批准的表单都存储在JIRA中，以便在需要时可以随时访问。我们已经映射了JIRA工作流，并将其呈现给CBIIT，以告知他们对构建的想法。4 .扩展GDS异常请求的提交、审核和审批平台。从2019年7月9日至2020年7月8日，CCR用户门户活动包括70个审核的GDSP和37个批准的GDSP。此外，79个IC进行了审查，其中63个IC获得批准。调查员资源Calzone博士和Logan Manlove都是CCR调查员的主要联系人。他们都参加了NIH科学政策数据共享办公室和NCI数据共享办公室的定期会议，以了解将影响CCR研究人员的政策的新发展。目前，两家公司都在与病理学实验室的调查人员合作，后者正准备提交一份例外请求。他担任物流、计算机和门户问题的负责人，由他处理。他接受过培训，现在在Calzone博士的监督下，对门户网站上提交的GDSP和IC进行初步审查，如果需要修改，他会及时向研究者提供反馈。他是进入dbGaP研究注册的领头人。他还在数据共享过程中支持调查人员。他曾努力与CBIIT和dbGaP的关键人物建立联系，这大大提高了代表调查人员对查询的响应时间。他维护CCR GDS Wiki页面，这是CCR调查人员的在线GDS关键信息源。Manlove先生还维护JIRA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。Calzone博士从事GDS的监管方面的工作，其中包括今年在IRBO建立的一个委员会任职，以改进GDS的标准同意语言。随着政策的更新，包括公众访问GSR数据，她领导了CCR敏感性审查委员会。一旦所有现有的研究都确定了GSR敏感性，并且委员会明确了确定标准，就会在Manlove先生的帮助下将其过渡到在线系统。Calzone博士审查所有提交的决定，并与委员会讨论是否存在问题。她在iRIS中及时输入所有最终灵敏度测定，以便进行科学审查。当需要与NCI数据共享办公室联系时，Calzone博士充当接口。最后，她维护和更新所有CCR GDS sop。新研究：从iRIS （n=107）或年度报告（n=7）中确定了114项新研究。经过与研究者的审查和讨论，其中80项研究仍然适用GDS。合规跟踪研究：过去一年有62项GDS适用研究已关闭或正在进行数据样本/分析。在吉拉有183项正在进行的研究。GSR敏感性测定：共回顾了99项研究，其中26项敏感，73项不敏感。dbGaP活动：今年在dbGaP中注册了334项研究，其中321项是最小注册，12项是完全注册。从dbGaP中删除了两项研究。数据共享：共有6项研究完成数据提交并发布。还有5项研究提交了新版本的数据。有几项研究正在提交数据，其中：5项正在等待表型和测序数据；3 .等待分子数据和测序数据；3 .等待测序数据；3 .等待表型数据；4 .初始表型数据集与表型数据字典文件未提交；将提交的数据转移到受控访问。

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 the following documents dependent on whether the study involves human or non-human organisms or cell lines. The Genomic Data Sharing Plan (GDSP) form 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 Institutional Certification (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: 1-maintaining and updating user groups 2-IC memos sent through the portal were at times failing to generate a copy of the submission. A copy of the submission packet is saved before being sent to the mid server to generate the final IC PDF. If the PDF generation fails, we would regenerate the IC packet for the team but the investigator would have to sign the same IC sometimes multiple times. This issue took multiple weeks to identify the source of the problem and resolve. Beginning in July, 2020, CBIIT launched an effort to further enhance the portal. We are currently meeting weekly to address the following items: 1-GDSP's originally generated and approved in portal version 1 have been stored unattached to a project in the version 2 portal. The first priority is to establish projects that correspond to each GDSP with project specific team access based on the original submission. 2-Address portal login issues. For the GPA and GPA Admin, the portal can take greater than 5 or more minutes to load. This is not an issue for end users entering forms, but an issue for those with access to all projects. 3-Merge the JIRA tracking database into the portal. Currently, JIRA is the platform used to track GDS project status and generate reports. However, this results in similar data being stored in two locations. Given the portal login issue and limited search function in the portal, all approved forms are stored in JIRA so they can be readily accessible when needed. We have mapped the JIRA workflow and presented it to CBIIT to inform their thinking on the build. 4-Expand the platform for submission, review, and approvals for GDS exception requests. CCR user portal activity from 7/9/2019-7/8/2020 consisted of 70 GDSP's reviewed and 37 GDSP's approved. Additionally, 79 IC's were reviewed with 63 IC's approved. Investigator Resource Both Dr. Calzone and Logan Manlove serve as the primary contacts for CCR investigators. Both attend the NIH Office of Science Policy Data Sharing and the NCI Office of Data Sharing periodic meetings to learn about new developments in the policy that will impact CCR investigators. Currently both are working with investigators in the Laboratory of Pathology that are preparing to submit an Exception Request. Mr. Manlove serves as the lead for logistical, computer, and portal issues are handled by Mr. Manlove. He has been trained and now under Dr. Calzone's supervision does the initial reviews of GDSP and IC submissions in the portal, providing timely feedback to investigators if modifications are required. He is the lead on entering dbGaP study registrations. He also supports investigators in the data sharing process. He has worked to establish contacts with key individuals in CBIIT and dbGaP which has greatly enhanced the response time to queries on behalf of investigators. He maintains the CCR GDS Wiki page, the online GDS key information source for CCR investigators. Mr. Manlove also maintains the JIRA tracking database enabling rapid response to investigator queries about the status of a given project or any possible report requests. Dr. Calzone works with the regulatory aspects of the GDS which included this year serving on a committee established by the IRBO to improve the standard consent language for GDS. With the update in the policy to include public access to GSR data, she leads the CCR Sensitivity Review committee. Once all existing studies had a GSR sensitivity determination in place and the committee was clear on the determination criteria, this was transitioned with the help of Mr. Manlove to an online system. Dr. Calzone 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. Lastly, she maintains and updates all the CCR GDS SOPs. Data Sharing Update-Statistics from 7/9/2019-7/8/2020 New Studies: There were 114 new studies identified from either iRIS (n=107) or annual reports (n=7). After review and discussion with investigators, 80 of these studies remain GDS applicable. Studies Tracked for Compliance: This past year 62 GDS applicable studies were closed or are in data specimen/analysis. There are 183 active studies being tracked in Jira. GSR Sensitivity Determinations: A total of 99 studies were reviewed, of which 26 were Sensitive and 73 Not Sensitive. dbGaP Activity: This year 334 studies were registered in dbGaP of which 321 were minimal registration and 12 full registration. Two studies were deleted from dbGaP. Data Sharing: A total of 6 studies completed data submission and the data were released. There were also 5 studies with new versions of data submitted. Several studies have data submission in process consisting of: 5 waiting on phenotype and sequencing data; 3 waiting on molecular data and sequencing data; 3 waiting on sequencing data; 3 waiting on phenotype data; 4 initial phenotyping data set with the phenotyping data dictionary files not submitted; 1 moving submitted data into controlled access.