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。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。去年与门户相关的活动包括对门户（版本3）的增强，解决了以下问题：1-最初在门户版本1中生成和批准的gdsp已单独存储在版本2门户中的项目上。这需要建立与每个GDSP相对应的项目，并基于原始提交的项目特定团队访问权限。改善门户登录问题。对于GPA和GPA Admin，门户的加载时间超过5分钟。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。系统对GPA和GPA管理仍然很慢，但得到了改进。3 .为门户创建一个跟踪数据库臂，因为NCI将不再支持JIRA程序，NCI将作为原始跟踪数据库。门户的跟踪臂已经创建，包括报告功能，经过可用性测试，所有现有数据上传到系统并审计准确性。从2020年7月9日到2021年7月8日的统计数据：跟踪门户：共有505项研究驻留在新的GDS跟踪门户中，本报告期间有86项。在本报告所述期间，审查了40个GDSP和46个IC，并提交了一个例外请求。新研究：从iRIS （n=61）或年度报告（n=16）中确定的77项新研究。基因组总结结果敏感性测定：61项研究回顾了基因组敏感性测定，其中18项敏感，43项不敏感。dbGaP注册：439项研究注册，105项在本报告期内。其中71个是最低登记。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项研究正在提交数据，其中1项正在等待分子数据和测序数据；1等待分子数据；1等待测序数据；8人等待表型数据。14项研究在没有数据共享的情况下结束。研究者资源：Calzone博士担任CCR基因组项目管理员（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，现公布该职位。在此期间，所有活动都由卡尔宗尼医生负责。所有由曼洛夫先生完成的dbGaP注册已被重新分配给卡尔宗尼医生。GPA和GPA- a的作用包括参加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研究者的新政策发展。Calzone与GDS监管方面的工作，其中包括开发和呈现GDS培训会议为NIH的校内调查人员在12/1/2020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。她还处理任何CCR例外请求，今年涉及病理实验室的研究人员，这是一项处于批准最后阶段的请求。最后，她维护和更新所有CCR GDS sop。GPA-A负责后勤、计算机和门户问题。一旦被聘用，GPA-A替代者将接受培训，并在Calzone博士的监督下工作：在门户网站上完成对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，并输入dbGaP研究注册并支持研究者进行数据共享过程；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。

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.