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Submitting your genomic data to NCBI’s database of Genotypes and Phenotypes (dbGaP)

Below are instructions and a collection of resources we’ve put together to help guide you through the dbGaP submission process. Please keep in mind that this is a lengthy process that may take several weeks.

It is our recommendation that the first thing you should do is obtain IRB forms. These forms are required in order to complete the first step in the submission process and can be a rate-limiting step, so we strongly advise that you work to obtain these as soon as you know you will be submitting.

In order to create a project in dbGaP and upload data files to accompany a publication, the IRB needs to review all cases to ensure everyone was properly consented. The MSK IRB will then send an institutional letter to dbGaP to officially register the project.

For all studies:

You must fill out the dbGAP submission form available from the MSK website. The form is under the ‘Genetic Research’ tab, then select ‘Genomic Data Sharing (GDS)’.

The dbGAP submission form is for an IRB request to certify that the data sets being sent are in compliance with the NIH policy before our IO signs the NIH certification letter.

For reporting germline incidental findings uncovered in your lab:

To receive the IRB forms required for dbGaP submission, you may download the forms here under “Category: Protocol Development, GAP Submission Form” or send an email to: IRBPB_Submissions_A@mskcc.org OR IRBPB_Submissions_B@mskcc.org. For assistance, please call the IRB/PB main number: 212-639-7592 For additional questions on the dbGaP submission process from study registration -> data submission -> study release, please refer to this instructional chart here.

Overview

dbGAP submission process pdf: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?document_name=HowToSubmit.pdf

1.       Register Study and Samples with dbGaP

2.       Provide Submission information via XML or Spreadsheet to SRA

3.       Upload Read Data Files

4.       Confirm Data Counts

Please keep in mind that this may be a lengthy process taking several weeks.

If it is NIH funded: send an email to your program officer or genomic program administrator and let them know you will be doing a submission

If it is NOT NIH funded – follow this information.

In order for your dataset to be considered, the steps below should be followed:

• Complete the basic study information form. Instructions for completing the form can be found here.
• Identify the NIH IC that most closely aligns with your research and include the IC name with the basic study information. http://www.nih.gov/icd/
• Indicate whether your study has been published or accepted for publication. If so, please provide documentation (i.e., the publication citation or a copy of any correspondence indicating that an article about the study has been accepted for publication).
• In order for your request to be considered, we will need to receive a certification signed by you and an institutional official.  Your institutional official is typically the person who signs your funding applications and is registered in eRA Commons as an authorized Signing Official for your institution. If no one from your institution or organization is registered in eRA Commons, information about this system is available from the eRA Commons website.  Also, NIH has developed Points to Consider for IRBs and Institutions to assist institutions in their review and certification of an investigator’s plan for submission of data to dbGaP.  The review of your request can be initiated without the certification, but the review process will be expedited if we receive the certification at time of submission.  The specific information that needs to be provided is explained in the attached documents.  To submit the required information, you may use the sample documents or any other format.
• Submit all information and the certification to GWAS@mail.nih.gov.

Once you have submitted this information, the information will be reviewed by the GWAS Program Administrator Analyst (GPA Analyst) to make sure they have all of the required information. The GPA Analyst will then send the basic study information to the NCI’s Review Subcommittee. This subcommittee will have a week to review the information and comment on the value of making the data broadly available to the scientific community, as well as consider the costs and the administrative burden of accepting the study.

After the subcommittee makes its decision, the GPA Analyst will notify the submitting investigator of the decision. If the study is approved, the GPA Analyst will register the study in the dbGaP system, and notify dbGaP personnel of the new registration. dbGaP staff will contact the submitting investigator directly to guide the investigator through the rest of the submission process.

Below is a sample email notifying the investigator that their study has been registered in dbGaP:

A dbGaP accession number will be assigned once dbGaP staff has received the completed study configuration files.

 -email the NIH (sra@ncbi.nlm.nih.gov; stineaj@ncbi.nlm.nih.gov) and tell them we will be doing a spreadsheet submission.

-Someone at the NIH will send back a spreadsheet for the PI to fill out

-Fill it out and return it

-This is the email we received in response: