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Data Commons Pilot Phase Consortium (DCPPC)

Instructions for Online Data Access Request (DAR)

Feb. 2, 2018

Overview

For a general overview of the dbGaP Data Access Request and approval process, please watch this video (it is very helpful).

In short:

  1. You complete an online application on the dbGaP web site.

  2. Your Institutional Signing Official (SO) signs the application and submits to dbGaP

  3. You will receive email notifying you about interim steps in the process

  4. The request is reviewed by the NHLBI and NHGRI Data Access Committee (DAC), which will be prepared to consider requests for DCPPC access using the generic template provided below.

  5. Both the requesting PI and SO will be notified by email of approval or disapproval.

Separate access requests must be filed by each institution funded under the DCPPC ROA, including subcontract institutions under an OT award. Multiple data sets may be requested simultaneously using one "project". Additional data set requests may be made at a later time using the same project.

The application must be updated if there are any changes in status, such as moving to another institution, adding or removing Internal Collaborators, and/or IRB approval status.

Pre-requisites for submitting an application:

  1. The applicant's name must be included in a list of DCPPC investigators eligible to submit DARs. This Master List of DCPPC investigators will be compiled during the time that investigators are submitting DARs for the datasets that don't need IRB approval (see #5 below).

  2. The applicant should be a senior investigator who will be responsible for proper use of the data by others at the same institution with whom the data will be shared.

  3. The applicant must have an eRA Commons account

  4. The applicant must have a dbGaP account in good standing; a dbGaP account is automatically created once you log in with your eRA Commons ID.

  5. Accession numbers for each of the data sets to be requested are listed in Appendix 1. These accessions will be requested in two separate phases:

  6. Phase 1: Prior to obtaining IRB approval, all data sets that do not require IRB approval will be requested (see "IRB" column of Appendix 1) there are 8 such accessions which are highlighted in green.

  7. Phase 2: After obtaining IRB approval, all data sets in Appendix 1 will be requested. These can then be added to the existing DAR from #5a under the same project, a separate DAR will NOT be required.

  8. IRB approval for the dbGaP accessions to be requested: Information for the IRB application:

  9. The type of IRB approval required is 'full' or 'expedited'; an IRB determination that the proposed research is 'exempt' or 'not human subjects research' does not fulfill this requirement.

  10. Request approval for all data sets in Appendix 1. Even though dbGaP does not require IRB approval for some of these, your IRB may need to know about them.

  11. IRB applications should note that some of the datasets to be requested contain data from sensitive populations. These include relatively small and geographically-restricted populations for which identifiability is an issue (e.g. the Framingham Heart Study and the Old Order Amish study), and studies of children (e.g. SAGE study of asthma in African American children); see "sensitive_pop" and "children" columns in Appendix 1.

  12. The IRB application title should be similar to that of the dbGaP application. It must be clear that the IRB approval is for receiving data for DCPPC infrastructure development; use "NIH Data Commons Pilot Phase -- Infrastructure and Development" in the title.

  13. There must be more than 3 months remaining on an IRB approval expiration date for the project request to be considered.

  14. Some IRBs require that all personnel in the applicant's group have Human Subjects training.

NOTE REGARDING IRB APPROVAL: NIH is exploring ways to simplify the IRB approval requirement at each institution, including the establishment of a central IRB for DCPPC investigators. Updates will be shared soon.

Application Instructions

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  • Go to dbGaP home page

  • Click on "Controlled Access Data" Log in with your eRA commons ID

  • Under "My Projects" tab, click on "Create New Research Project"

  • Click "Begin New Research Project" (bottom of page)

"Choose Datasets" tab


Appendix 1 contains the list of datasets that will be requested by DCPPC members. There are two types of datasets in this list: ones that require IRB approval in order to be accessed, and ones that don't. This is reflected in the "IRB" column. The 8 datasets that don't need approval from your IRB are also highlighted in green. Initially all DCPPC groups can request the 8 green datasets without needing IRB approval. Then groups can get approval from their IRBs for the other datasets and then add them to the DAR once they have approval. This requires a modification of the DAR which is fairly straightforward. If you already have IRB approval for all of the datasets, you can request approval for all of them at the same time. It is VERY important that all DCPPC applicants have dbGaP approval for the same set of accessions.

In the "Choose Datasets" tab, you will see a long list of consent groups with check boxes next to them. Search for a "phs" accession number from Appendix 1. Some of these accessions have multiple consent groups, each with a separate box to check. Check ALL of the boxes (consent groups) available for a given accession number (e.g. phs000951 has two boxes). When you have clicked all of the appropriate boxes, go to the bottom of the page and click the "Add Selected and Continue" button. This will take you to the "Research Project" tab. You will have the opportunity to add more datasets later in the application process.

"Research Projects" tab


  1. "Descriptive Title of Project" -- Please use exactly this title:

NIH Data Commons Pilot Phase -- Infrastructure and Methods Development

  1. "Type of Research" -- If you see this section (you may not), check "Other" and then add this text to the box below: NIH Data Commons Pilot Phase - Infrastructure and Methods Development Application

  2. "Research Use Statement" -- please add the generic Research Use Statement in Appendix 2, exactly as given. This statement is longer than the 2200 character limit indicated in the form, however we have approval for it to be longer. Copy it exactly as it is in Appendix 2.

  1. Check the box under the Research Statement labeled "I am requesting permission to use cloud computing...." This will cause a "Cloud Use Statement" box to appear. -- Enter the Cloud Use Statement from Appendix 2.

  1. "Non-technical summary" -- Paste the Non-Technical Summary text from Appendix 2 in the box.

  1. "Choose your Signing Official (SO)" - You will see a list of Signing Officials for your institution. Check appropriate name (most Departments have a specific SO assigned to its members)

  2. "Applicant organization" -- Add your institution's name and address

  3. "Create Decryption Password" -- create a password as instructed

  4. Click "Save and Continue" box at the bottom of the page

  5. Since you selected cloud computing, you will be taken to the "Cloud Providers" tab.

"Cloud Providers" tab


There will be three different Cloud Providers for this project: Amazon Web Services, Google Cloud Platform, and Microsoft Azure. For each of these you will need to provide Name, Type, and Details. Type is always "commercial". Text for the Details section is in Appendix 2. Use the "Add Another" button to get information boxes for all three clouds. Fill in all of the information and then click "Save and Continue".

"Collaborators" Tab

  1. Provide names and contact information for Internal Collaborators --i.e. colleagues at your institution who will share access to the data obtained via this application. Trainees, lab staff or postdocs need not be named individually, unless they are not under the direct supervision of the applicant.

  2. "Are you planning to collaborate with investigators from other institutions?" This is the section where you will enter any subcontractors that are under your individual award. Uncheck "None". Then you will see a box for adding the names and contact information for External collaborators. Enter the names and contact information for each of the PIs and Co-Investigators on any subcontracts to your award.  If you do not have any subcontracts in your award, you can leave "None" checked and proceed to "Save and Continue".

  3. Click "Save and Continue" box at the bottom of the page

"IT Director" tab


Enter name, position/title, organization, address, email and phone for an institutional-level IT director at your institution.

Click "Save and Continue" box at the bottom of the page

"Choose Datasets" tab


This is the same page that came up earlier. You can add more datasets now if needed.

"Confirm Datasets" tab


  1. Check the list displayed to be sure it contains each of the accessions you need. Remember that AT LEAST all of the accessions in Appendix 1 that do not require IRB approval (highlighted in green) must be in this list. If you have IRB approval, then it should include all in Appendix 1. It is VERY important that all DCPPC applicants have dbGaP approval for the same set of accessions. If you missed any, you can click the "Back" button to return to "Choose Datasets".

  2. Then click "Remove Selected and Continue". This will not remove any of the accessions in your list unless you have selected "remove" in the drop-down menu for a given accession.

"Review DUC" tab


Read the "Data Use Certification Agreement" for each accession. All data uses through this application will need to follow the terms in these documents.

"Program-specific required attachments" -- If you have selected any datasets that require IRB approval (NOTE: this will be during the second round of requests, not during the initial request when only non-IRB datasets are being requested), a list of those will appear. You can upload an IRB document for each one separately, or you can upload one IRB document for all requests (generally, you will want to do the latter). For uploading one IRB document, skip over the set of boxes containing studies requiring IRB approval and check the box next to "Load one document for all requests" to upload a single document for all requests and browse to its location. You may need to scroll down to the bottom of the page to see this box (see screen shot below).

Note that the type of IRB approval required is 'full' or 'expedited'. An IRB determination that your proposed research is 'exempt' or 'not human subjects research' does not fulfill this requirement.

Upload a pdf that has your IRB approval and the Master List (Appendix 3) of DCPPC members. Both of these are required for the approval process. The requested IRB approval document is your local institutional IRB approving use of the data sets for the DCPPC project and the title of the IRB project must make this clear. Check your IRB document to be sure that it has more than 3 months before expiration. The IRB approval letter must be addressed to you or to one of the Internal Collaborators named in your application. You will be allowed to upload just one file, so concatenate the IRB approval and the Master List of External Collaborators (DCPPC members, Appendix 3) into a single pdf file. Then click "Upload Selected files".

Note for possible future dataset requests: When requesting studies with a Collaboration consent group (COL) modifier, an approval letter from that study's data set contacts must be appended to the IRB approval document. None of the Tier 1 datasets in Appendix 1 have this modifier, so this should not arise in initial stages of DCPPC.

"Review DUL" tab


For each requested data set, click the box "I understand and agree...", indicating your agreement, based on the documents in the previous section and the stated Data Use Limitations.

Click "I understand and agree to the terms..."

"Review Applications" tab


  1. Click on the pdf icon labeled as "Review Complete Application" and review it.

  2. Check the two "I agree" boxes to provide the required certifications and assurances.

  3. Click "Submit Application to Signing Official" button.

Following status

You will receive automated emails indicating status of application approval. You can also check status by clicking the "My Requests" tab after logging in with your eRA Commons ID

Do NOT email DAC members with notification that you have submitted an application. They will see it as it comes through the dbGaP system.

Appendices

Appendix 1. Table of dbGaP accessions to be requested by OTA awardees for Tier 1 access

Appendix 2. Generic text for Tier 1 Data Access Requests

Appendix 3. (NOTE: this will not initially be available) Master List of DCPPC investigators participating in Tier 1 access. Information for this will be collected during the first DAR submissions of non-IRB datasets. Thus, it will not be available immediately.