Genomic Data Sharing

基因组数据共享

• 批准号: 10262783
• 负责人: Kathleen Calzone
• 金额: $ 89.34万
• 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/10262783
• 关键词: Address; Adopted; Affect; Animal Experimentation; Animal Model; Annual Reports; CCR; Cell Line; Certification; Clinical Protocols; Clinical Research; Computers; Consent; Consent Forms; Data; Data Set; Databases; Development; Disease; Ensure; Environment; Feedback; Funding; Gene Expression; Generations; Genome; Genomics; Human; Human Cell Line; Individual; Infectious Agent; Informed Consent; Infrastructure; Iris; Laboratories; Language; Lead; Learning; Location; Logistics; Maintenance; Malignant Neoplasms; Maps; Metagenomics; Modification; Molecular; Natural regeneration; Nursing Research; Online Systems; Organism; Participant; Pathology; Periodicity; Persons; Phenotype; Policies; Process; Protocols documentation; Rare Diseases; Reaction Time; Reporting; Research; Research Personnel; Resources; Retrieval; Review Committee; SNP array; Science Policy; Services; Source; Specimen; Supervision; System; Thinking; Time; TimeLine; Training; United States; United States Food and Drug Administration; United States National Institutes of Health; Update; Work; base; data dictionary; 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; prospective; rare cancer; repository; response; statistics; transcriptomics; 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 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.