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TOPMed Paper Proposal Instructions

TOPMed manuscript authors are encouraged to use the TOPMed Author Checklist to track their progress through the TOPMed publication process as described below. The checklist is also designed to give authors a sense of the time it takes to complete each step.

Analysis of data from studies other than your own should not begin until all of these steps have been completed and approvals obtained.  The status of your proposal is summarized on your Dashboard.

Steps for TOPMed paper proposal development and approval

Proposal development occurs within the context of a TOPMed Working Group. The proposer should outline the basic aims of the paper, questions to be addressed, the analytical approach, and what data sets will be used. These issues will be discussed within the Working Group, along with collaborations and authorship. Proposers should discuss authorship with contributing studies, ACC, IRC, and sequencing centers see (TOPMed Publications Policy on collaboration and authorship.) Working Groups will discuss and resolve potentially overlapping or competing proposals. In these discussions, priority must be given to proposals that address the aims of the studies that were selected for inclusion in the TOPMed program and are focused on that study’s own data. However, cross-study proposals that maximize the value of the TOPMed program as a whole are strongly encouraged.

If a Working Group does not respond to a proposal submission within two weeks (by at least scheduling a discussion), contact the ACC, which will look into the situation and refer problems to the Executive Committee as needed.

Working Group approval is not required for “single PI” proposals in order to submit to the TOPMed system. However, proposers are required to circulate these products to the WG for informational and tracking purposes. Proposers are also encouraged to present to the WG at the discretion of the convener(s).

The Ancillary Working Group acts as a home for paper proposals that do not fit into other TOPMed Working Groups. As with other Working Groups, please contact the convener(s) prior to submitting a proposal under the Ancillary Working Group.

Currently, there is no formal process for Working Group approval. However, Working Groups' conveners are encouraged to record group approval by sending an email to the paper proposer, which can be forwarded to the study PIs along with their request for approval to use data.

Working Group members access TOPMed data through senior members of the TOPMed Project or center with which they are affiliated. Each TOPMed Project or center has designated a limited number of individuals who are eligible to apply for access to data in TOPMed Exchange Areas. The Exchange Areas provide for data sharing among TOPMed investigators prior to those data being released on dbGaP for access by the general scientific community. The eligible applicants may share these data (from multiple TOPMed studies) with collaborators at their own institution. Individuals planning to submit TOPMed paper proposals should discuss with leaders of their study how they access the data that they need to complete the analyses proposed. In many cases, the analyses will be collaborative and involve several working group members. Each member of the analysis/writing group should plan access mechanisms in advance of submitting a proposal.

Requests for initial PI approval for use of data from their study should be made by email from the proposer to the PIs of the parent studies whose data is being analyzed and their associated TOPMed Projects. Contact information for these groups are provided on the individual study pages. The email should include a draft of the proposal, a request for collaboration and a statement that a Working Group has approved the proposal concept. Also, the email should name investigators from the PI’s study with whom the proposer has communicated already about collaboration. Please ask the PI to indicate whether there are any consent groups that should not be included in analyses due to data use limitations of particular consent groups in the context of your paper proposal.

The PI has two weeks to respond to this request. S/he may approve, disapprove or request modification. If there is no response within two weeks, the proposer may proceed with submission. The PI will have another chance to approve/disapprove during the subsequent selection of data sets (i.e. study-consent groups), when s/he can also view the submitted version of the proposal. The reasons for having two PI approval steps are: (a) in the initial step, PIs have a chance to request modifications of the proposal before it is submitted for scientific review; and (b) PIs' studies may not have been registered at the time of proposal submission, in which case, selection of specific study-consent groups must occur after the proposed analysis is underway.

Proposals are submitted using the online form. This form includes selection of the TOPMed Projects the proposer and the studies’ PIs have already agreed will contribute data to the analyses (specific consent group selection occurs in the next step). The proposer will certify that s/he has obtained approval from a Working Group and that s/he has contacted the PIs from each of these TOPMed Projects and their associated parent studies.

The TOPMed member who submits the proposal to the website is the "submitter". The proposal submitter must be a TOPMed member, and can view the proposal in his/her dashboard, manage data set requests, and update the proposal's progress report. Within the proposal submission form, the submitter should note a "proposer" who is the TOPMed scientific lead for the proposal. The proposer should be a TOPMed member and can be the same person as the submitter; the proposer does not need to be the first author on the paper. The submitter may include an addtional TOPMed member as a "designated updater", which grants that person the same permissions to view and manage the proposal as the submitter (the designated updater can view the proposal in his/her dashboard, manage data set requests, and update the proposal's progress report).

The Publications (P&P) Committee reviews each submitted proposal through an online forum. Each paper proposal is posted to the review forum, and an email link is sent to each voting P&P reviewer. Reviewers have 14 days to review the proposal, and to enter one of four recommendations:

  • Approve (may append comments)
  • Reconsider after revision (describe specific concerns)
  • Conflicted (indicate what sort of conflict of interest the reviewer has with the proposal)
  • Disapprove (state reasons).

Reviewers are given two weeks to respond. The proposer will be informed of the P&P’s decision and will receive anonymized reviewer comments.

With a review status of "disapprove" or "reconsider after revision," the proposer will not be able to move forward with the proposal until a revised version is submitted, which will trigger another round of scientific review. Proposal revisions can be submitted through the same online form as the original submission, by selecting your proposal from the drop-down menu under “If you are resubmitting a proposal, please specify the original in order to avoid duplicate proposals”.

Approved proposals will be posted in a publicly accessible P&P archive. For the duration of the TOPMed program, any submitted abstract or manuscript using TOPMed data must be associated with an approved manuscript proposal.

After proposal submission, proceed to the request datasets webpage to select datasets, on which you will select specific study-consent groups to be used. Only parent studies that have completed dbGaP registration will have their data sets displayed here for selection. If you plan to use data sets from an unregistered study (i.e. having selected it on the proposal form), you will be notified when those consent groups are available for selection. You will then need to return to this page and add those selections.

Each data set corresponds to a single dbGaP consent group within one parent study of TOPMed, and is indicated by a single check box. It is very important to read the Data Use Limitations displayed for each data set. When you have finished the selection, you will check a box confirming that you understand and will abide by the consent limitations described therein.

When you select a data set, an automated email will be sent to the appropriate PI(s) or his/her designees, who will either approve or deny use of their data sets for this paper. If the contacts have not responded within 14 days, your request will be automatically approved.

Provide regular updates on the progress of your paper proposal via the Progress Report Form.

Refer to the TOPMed Manuscript Writing and Submission Instructions when the proposal progresses to the manuscript stage. Manuscripts must be submitted to the TOPMed website, linked to their associated proposal, prior to submission to a journal.

Every approved TOPMed paper proposal has an associated progress report to track the paper’s progress. Keeping progress reports up-to-date has several benefits:

  • It ensures an accurate list of active TOPMed paper proposals.
  • It helps Working Groups track progress and offer assistance as needed.
  • If the original proposal team stops work on their proposal it can be marked as “inactive”, allowing other TOPMed investigators to see the history of the proposal and continue research in that area if appropriate.
  • Details about a paper’s progress helps point to process issues and improvements.

Progress reports can be accessed through the proposal submitter's Dashboard, via the Paper Proposal viewer, and on the Paper Proposal Progress Report page. Progress reports are viewable in full by the proposal submitter, the designated updater, the primary Working Group conveners, and the TOPMed ACC. Other registered TOPMed users may view only the status section (initial questions 1-15). To submit confidential or sensitive feedback directly to the ACC, please see the "Proposal and manuscript submissions" row of the Key Contacts Page.

The progress report form should be updated by the proposal submitter or the designated updater regularly: minimally every six months, per TOPMed Publications Policy. It can also be updated by a convener of the proposal’s primary Working Group or by the TOPMed ACC (all updates should be done in collaboration with the original proposal team whenever possible). The proposal’s “active” or “inactive” status should always be kept up-to-date. The progress report should also be updated with progress details whenever tasks are completed. Proposals that have had no a status update for more than six months may be marked as “inactive” by the primary Working Group conveners or TOPMed ACC.

To update the progress report for paper proposals you have submitted or for which you are the designated updater:

  1. Navigate to your Dashboard on the TOPMed website.
  2. Make sure the “Paper Proposals” tab is selected. (If you are both the submitter and a designated update for a given paper proposal, you will see that proposal listed twice.)
  3. For each listed paper proposal, click the “update now” text within the “Progress Report Last updated” column to edit that proposal’s progress report.
  4. Near the top of the progress report form, you will see a section titled “Proposal Status Confirmation”. At minimum, please indicate whether the paper proposal is “Active” or “Inactive”. Paper proposals that have an associated publication noted on the TOPMed Publication Page are not considered “inactive” and should not be marked as such.
  5. Provide additional information including details about the status and which tasks have been completed. Tasks are listed in anticipated chronological order (though some may be done in parallel), with the exception of two methods-paper-specific tasks (#14 and #15).
  6. Click the “Save” button at the bottom of the form.

Paper proposals with an “inactive” status are viewable by all TOPMed members on the Inactive Paper Proposal Viewer. Inactive proposals can be reactivated at any time by the original proposal team, or by a new proposal team with permission from the primary Working Group. If you have questions about a paper proposal on the inactive list, please contact the primary Working Group conveners.