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dbGaP
This documentation is meant to summarize the procedure for the submission of data to the dbGaP repository. You are encouraged to review the dbGaP Study Submission Guide from NCBI, which covers all aspects of the submission process in detail. This dbGaP Flow Diagram provides a high-level overview of the submission process. The submission of study data into dbGaP is a two-step process: study registration and data submission.
NCBI provides a db GaP Registration Guide, which covers each step of the registration process in detail. A summary of this process is provided below. The study registration process should be initiated by the PI of the study.
1. Identify the appropriate GPA (Genomic Program Administrator)
Each funding institute or center (IC) has designated staff, referred to as GPAs, who assist researchers with the process of registering a study and submitting genomic data. A list of current GPAs for each funding institute or center can be found here. A GPA is a required part of the registration process. Researchers cannot register a study without using a GPA. This may be a two-step process. First find the associated NIH grant (for example an NIH NCI grant) and determine which division/center it falls under. Then, look up the appropriate GPA for that NIH center. For NCI grants the GPAs are listed here
These study registration steps provided here pertain to NIH-funded studies. For non-NIH funded studies, please refer to How to Submit A Non-NIH funded Study to dbGaP for step-by-step instructions. If your study is funded by the National Institute of Neurological Disorders and Stroke (NINDS) you can look at this guideline document. Some example completed registrations are available in the ICTS WUSTL Grants Library.
2. Ensure that study participants are properly consented
If you plan to submit genomic data to dbGaP (or to another repository for broad sharing), be sure that you are properly consenting participants for broad data sharing. All consent form versions that were actually used to obtain consent from participants to create the genetic/genomic data will be reviewed by the IRB prior to providing institutional certification for the data submission. For guidance on consent for genomic data sharing, see the ICTS Precision Medicine website here: https://ictsprecisionmedicine.wustl.edu/guidance-best-practices/consent-for- genomic-data-sharing/
3. Obtain an Institutional Review Board (IRB) for a signed Institutional Certification
Before submitting any data, it is necessary to prepare and obtain an institutional review board (IRB) for a signed Institutional Certification for NIH funded studies. Additional information on completing an Institutional Certification can be found here.
The Human Research Protection Office (HRPO) at Washington University operates the SWAT! On-Call Service to help make the IRB review process more transparent and efficient. Through the SWAT! On-Call Service, HRPO staff are available to answer questions about the IRB review process, provide information on human subject protections, and support your use of myIRB
The SWAT! On-Call Service can be accessed at (314) 747-6800.
An On-Call HRPO staff representative is available to take your call Monday-Friday from 8:00 am to 4:00 pm.
What you will need to obtain an institutional certification letter
- Name of the individual to whom the certification letter should be addressed.
- Dates that samples were collected – before January 25, 2015; after January 25, 2015; not yet collected (select all that apply).
- Original source of samples – under the approved study; obtained from outside entity; collected without consent (only if prior to January 25, 2015) (select all that apply).
- Copies of all consent form versions that were used to obtain consent from participants (at this institution) to create the genetic/genomic data.
- Excel spreadsheet listing all consent forms that you are requesting the IRB to review for the institutional certification. This list should correspond with the file of scanned consent forms (previous bullet point). Specifically, for each consent form, you must list version date (date consent was approved by HRPO) and the number of individuals from whom data/samples were collected and requesting submission to dbGaP. The Excel spreadsheet is downloaded from the myIRB application.
- List of all data points or variables that will be submitted to dbGaP. Specific data points must be listed. Simply stating "demographics" or "clinical information" is not sufficient. This information is entered on a separate tab of the Excel spreadsheet.
4. Send the Required Documents and Information to the GPA
Once you have obtained an Institutional Certification, you should work on gathering basic study information that will later be entered into dbGaP during registration. A list of standard information gathered at this point in the process is provided below. Some funding institutes/centers (ICs) might require additional information at this stage. These details will be provided by the GPA.
- Target dates for data submission and data release
- Number of participants
- Data type
- Secondary contact information
- Consent groups
- Acknowledgement statement
5. The GPA Registers the Study in dbGaP
Once the basic study information has been received and the Institutional Certifications have been approved, the GPA will start the registration process in the dbGaP system using the PIs name, study name, and grant number (extramural) or protocol number (intramural).
6. The PI receives an "invite" from the dbGaP system
Once the GPA initiates the registration in dbGaP, the PI, or their designated subordinate, may receive an email with instructions for completing the study registration process.
7. PI completes the study registration in dbGaP
The PI, or their designated subordinate, will then enter the basic study information into dbGaP. This information can be updated as needed. The GPA will then upload the signed Institutional Certification and create a Data Use Certification in dbGaP
The Institutional Certification ensures that the study complies with the Genomic Data Sharing (GDS) policy and sets limitations, if any, on how other researchers can use the datasets.
NIH Funded Researches: Should already have completed a signed institutional certification submitted as part of Just In Time Process and prior to the award.
Non-NIH funded Researchers: will need to complete a signed institutional certification to accompany their study submission.
8. GPA verifies the study registration information
Once the GPA verifies the study registration in dbGaP, the PI, or their designated subordinate, will receive an email invitation to the dbGaP submission portal. The registration system then changes the study to "Complete" and locks the study to prevent further changes until the study is released.
Under the NIH GDS policy, large-scale human genomic studies must be registered with dbGaP, but the data can be submitted to dbGaP and/or another repository (e.g. AnVIL), in accordance with the approved GDS plan.
1. Data submission to dbGaP
For researchers who plan to submit data to dbGaP, there is a detailed study submission guide that covers all aspects of the data submission process and includes templates and instructions on how to format data files in preparation for submission
-After submission of metadata to dbGaP, the PI will receive a study accession number and a password-protected preview site to review and approve.
-The dbGaP team will then process and prepare the data.
-For data that will be submitted to a repository other than dbGaP, the study will have a public page on dbGaP with the metadata and provide access control to users, when necessary.
-After the PI approves the preview site, dbGaP will then publish a public display of summary-level data and controlled-access release of individual-level data.
-Studies that have been granted an alternate data sharing plan might not need to submit data to dbGaP, but are still required to register the study in dbGaP.
2. Data submission to a repository other than dbGaP For researchers who plan to submit data to a repository other than dbGaP
-It is still required to register the study with dbGaP.
-It is necessary to submit the associated metadata to dbGaP.