TOPMed Author Checklist

Pre-proposal submission [2-3 months]

• Familiarize yourself with the TOPMed Publications Policy, Paper Proposal Instructions, Manuscript Writing Instructions, and Guide for Using TOPMed Data.
• Review elements of the paper proposal submission form.
• Identify relevant TOPMed Working Groups (WGs). One WG must be the primary; additional WGs can be marked as relevant.
  • Develop proposal within the primary TOPMed WG. Email WG conveners (primary and relevant) with paper proposal idea.
  • [2 weeks or less] Request initial approval from PIs for use of data and for suggested co-authors; also contact ACC, IRC, and sequencing centers for suggested authors see (TOPMed Publications Policy on collaboration and authorship.)
  • Proposals are ideally presented and discussed at standing WG calls or discussed by email, dependent upon the desire of the WG conveners.
  • [2 weeks] Obtain approval from the primary and relevant WGs. Allow two weeks for responses from PIs and WGs.
• [1 month or more unless already in place] Discuss data access with your study’s leaders. See TOPMed Data Sharing Policies.
   

Proposal submission [2-4 weeks]

• Using the online form, submit proposal to the TOPMed website for scientific review by the TOPMed Publications Committee (P&P). See TOPMed Paper Proposal instructions.
• Submit dataset selections for review using the online form anytime after you have submitted the paper proposal. See TOPMed Paper Proposal Instructions.
  • You may request additional or newly available datasets at any point.
• [2 weeks] Await completion of scientific review, then review comments and approval status.
  • P&P approval is required before commencing work.
  • Please note: major revisions requested by reviewers may add days or weeks to this step (see Revise Existing Paper Proposal for more information).
  • Scientific reviewer comments are advisory only for "single PI" proposals, which are automatically approved after two weeks.
• [2 weeks or less] Once dataset selections are submitted online, await completion of dataset review. If dataset reviewers do not respond within two weeks, the dataset selections are automatically approved.
• Carry out proposed work.
• Regularly update proposal status on the paper proposal progress report page.
• Changes to work performed should be reflected in the manuscript proposal. Major changes (e.g. broadening of scope) require re-review.
• If requested by primary or relevant WGs, provide regular updates.
   

Manuscript submission [1-2 months]

• Review the TOPMed Publications Policy, Manuscript Writing Instructions, Guide for Using TOPMed Data, and your Paper Proposal Resource Page.
• [2 weeks] Request approvals and solicit authorship: the following manuscript preparation steps may be done separately or in parallel, but be sure to allow at least two weeks for each of these steps to be completed prior to manuscript submission.
  • Contact studies with co-authorship requirements, ACC, IRC, and relevant sequencing or omics centers to confirm relevant co-authors are included (see key contacts). Allow at least two weeks for responses before submitting the manuscript to the ACC.
  • Obtain WG approval(s) for the draft manuscript (see template). Allow at least two weeks for WG responses. WG approval is not required for single PI manuscripts, but a copy of the draft manuscript should still be provided to them.
  • Review the datasets approved for the associated paper proposal at least two weeks prior to submitting the manuscript to the TOPMed ACC. Make any needed dataset requests or cancellations to ensure that this list of datasets matches what was used in the manuscript.
  • Request study-specific approval(s) for the draft manuscript, giving study contacts at least two weeks to respond before submitting the manuscript to the TOPMed ACC. Attach any approval documentation you’ve received by the time of submission. If any studies have not responded to your request for review within two weeks, include a list of these studies, noting who you contacted and the date you contacted them. This step is not required for single PI manuscripts, though authors are still responsible for ensuring that study-specific approval processes are followed.
  • If any of the manuscript co-authors are NIH employees, please ask them to submit the manuscript for NIH review at least two weeks prior to submitting the manuscript to the TOPMed ACC.
• Add required acknowledgments, authors, and documentation text to the manuscript.
  • Extract from the Paper Proposal Resource page:
    • Sequencing/omics support information
    • Study-specific acknowledgements (not required for single PI manuscripts)
    • Study-specific descriptions (e.g., for methods sections)
  • TOPMed acknowledgements
  • TOPMed Banner Author List (not required for single PI manuscripts)
  • Include requested authors and the TOPMed banner text within the author list, as noted in the TOPMed Authorship Guidelines. (The TOPMed banner text is not required for single PI manuscripts)
  • Methods documentation, as appropriate
• Submit manuscript to TOPMed website for ACC administrative review.
• [3 business days] Await completion of ACC administrative review, then review comments and approval status.
  • Approval is required before submitting to the journal.
  • Please note: if any of the requirements listed above are missing from the manuscript, this may add days or weeks to this step.
• [7 business days] Once ACC administrative approval is granted, there is a seven business day final review period for dataset contacts of studies used in the paper. This review period must be complete before submitting to a journal.
• Submit to journal.
• Continue to follow-up with any groups that have not responded to previous requests for review (studies, NIH) or authorship (studies, IRC, ACC, Omics Centers), as subsequent revisions and journal (re)submissions may enable incorporation of any resulting requests.
   

Publication

• In accordance with the NIH Public Access Policy, upon acceptance for publication, submit an electronic version of the final, peer-reviewed manuscript to PubMed Central.
• Update ACC (topmed-pubs@westat.com) when accepted for publication.
• Note subsequent revisions, e.g. in response to peer reviews, do not need to be re-submitted to the TOPMed website. However, please contact the ACC (topmed-pubs@westat.com) if additional TOPMed datasets are used so we can update our records.
• Update ACC (topmed-pubs@westat.com) when published, noting PubMed ID.
• Optionally update the ACC (topmed-pubs@westat.com) if the paper is posted online as a preprint ahead of publication.