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dbGaP Registration Instructions for TOPMed

 

 

Introduction

Each of the TOPMed studies must register the Whole Genome Sequencing (WGS) component of their study at dbGaP.  Many TOPMed studies already have a ‘parent’ study in dbGaP, which contains phenotypes, array and/or other molecular data; in this case, the TOPMed WGS component will be a ‘child’ study under the ‘parent’ study and it will receive a separate ‘phs’ accession number. Some TOPMed studies consist of a consortium of sub-studies; in this case each sub-study must register separately.

Initially, the TOPMed studies will each exist in a separate ‘exchange area’, which is a pre-release version of the dbGaP accession available only to TOPMed study investigators. After QC and preliminary analyses, these studies will be released for access by the scientific community using the standard dbGaP application process. The temporary exchange areas also serve as mechanisms for file exchange among the various TOPMed studies, and IRC.

Sequence data (bam files) for each study will be deposited to the Sequence Read Archive (SRA) by the TOPMed Informatics Research Center (IRC).  Subsequently, the study investigator can access those files via their exchange area. No files can be deposited to dbGaP until registration is complete. Therefore, it is important to begin the registration process as soon as possible.

Overview of the main steps to complete registration:

  1. Contact NHLBI Genomic Program Administrator (GPA) to initiate study registration – study PI
  2. Obtain Institutional Certification – study PI with his/her institutional IRB and Signing Official
  3. Send Basic Study Information to GPA – PI
  4. Data Use Certification – NHLBI Program Officer or GPA
  5. Reviews information and approves further submissions- GPA
  6. Prepare the dbGaP Study Config and Data files – study PI

View dbGaP diagram ‌  and Flow Chart 1 ‌  (which has some TOPMed-specific elements).  Refer to the dbGaP Submission Guide ‌ .

 

Details

First, study PIs should contact their NIH Program Officer and the NHLBI GPA to initiate the process.  The study PI will receive an email from the dbGaP registration system with instructions on how to access the system and continue registration.  The following steps are required.  See table below for contact information for specified individuals.

  1. Contact the NHLBI GPAs (nhlbigeneticdata@nhlbi.nih.gov, NHLBITOPMeddbGaP@nhlbi.nih.gov) to initiate the process.
  2. Obtain Institutional Certification (IC) signed by PI’s institutional Signing Official. Download a blank IC form and instructions.
    1. Put in the name of the GPA at the top of the form.
    2. For address, at the top of the form, please use this, regardless of which phase your study is in: GDS Program Administrator, NHLBI, NIH, DHHS, 6701 Rockledge Drive, Room 10120, Bethesda, MD 20892-7936
    3. Use the GDS guidance Points to Consider in Developing Effective Data Use Limitation Statements . (Note for studies that already have “parent” level data in dbGaP, each individual person can have only one consent group and the data use limitations must also match.  If the parent study overall has four consent categories, though, the TOPMed study may have only selected a subset of these, which is permitted. Your assigned GPA can help as needed.)
    4. Send the IC as a pdf to the GPA, your PO, and the IRC (Tom Blackwell). The IC is generally reviewed by your institutional IRB before being signed by your institutional Signing Official. This can take time, so please start as soon as possible. Note: The limitations for data use must be clearly defined in the Institutional Certification.  The data use limitations must reflect the language of the informed consent document that each individual signed.  The data use limitations should influence the consent group designation for each individual participant.
  3. Prepare Basic Study Information – each study will need to complete a dbGaP Data Submission Information and return it to the GPA, and your PO.  The dbGaP Data Submission Information captures information regarding the study including: the submitting PI and Institution, a description of the study data, an acknowledgement statement to be used by secondary users when their analyses are published, and a basic description of the study.
    1. In Part I, under Study name, please use format "NHLBI TOPMed: [your study name]”.
    2. In Part V (Acknowledgment Statement), please include the following TOPMed-specific sentence and optionally your study-specific acknowledgement: "The TOPMed acknowledgement statement can be found at: acknowledgements. In addition, please include: [any study-specific acknowledgements for your study]."
    3. In Part VI (Original Summary of Study), please include a description of the study design of the original study as well as a clear description of how samples were selected for sequencing in TOPMed.
  4. Data Use Certification (DUC) – GPA will work with the PIs to create the DUC after receiving Institutional Certification and Basic Study Information from PI.  The data use certification agreement is the document that outlines the terms and conditions for secondary use of the data.
  5. GPA will review all submitted information and approve further submissions.  PI will receive an automated email on using the submission portal for uploading required files.
  6. Prepare the dbGaP Study Config and Data files for TOPMed.