Genomic Data Sharing

Division Of Basic Sciences - Nci

Investigators

Abstract

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.