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TOPMed Manuscript Writing and Submission Instructions

Preface

This document provides guidance from the TOPMed P&P Committee to authors and writing groups working on manuscripts that use study data. The layout is organized to follow the standard sections for publications so that the user can relate this material to their draft manuscripts. The details on how to submit a manuscript for administrative review are at the end of this document.

To assist with your manuscript submission, we recommend using your Paper Proposal Resource which is designed to aid manuscript authors with communicating and collating valuable study and working group information unique to each proposal. It may also be helpful to refer to the TOPMed Author Checklist, which provides an overview of the TOPMed publications process.

Guidelines

Title: Please consider using “TOPMed” in the title of your manuscript.

Authorship: Please refer to the TOPMed Authorship Guidelines and the TOPMed Publications Policy.

Sequencing methods: Please refer to the description of TOPMed Methods when writing this section and/or the TOPMed flagship paper pre-print.

Acknowledgements/Funding: Please use the TOPMed acknowledgment instructions.

Studies used in your manuscript may have additional acknowledgement requirements. It is incumbent on the lead author to ensure that these requirements are met. Please review the acknowledgement requirements for specific studies.

Use and reporting of race, ancestry, and ethnicity: Authors are encouraged to consult the Guidelines on the use and reporting of race, ethnicity, and ancestry in the NHLBI Trans-Omics for Precision Medicine (TOPMed) program when preparing their manuscripts.

Please complete the following steps at least two weeks prior to submitting your manuscript to the TOPMed website:

  1. Authors should begin by receiving Working Group approval for their manuscript. Other relevant Working Groups noted in the paper proposal should also review the manuscript, when applicable. Single-PI manuscripts don’t need Working Group approval, but the primary Working Group should be informed and a copy of the manuscript provided.
  2. As noted in the TOPMed Authorship Guidelines, please contact any required groups regarding co-authorship.
  3. Authors are required to submit the manuscript for study-specific review. Authors should keep records showing when they contacted each study, and include these records and any approval documentation received when submitting their manuscript to the TOPMed website. Single-PI manuscripts are not required to provide study-specific approval documentation.
  4. The NIH also has a review process that is required when one or more NIH authors are on the manuscript. Please ask one of the NIH authors to submit the manuscript to the NIH for review.
  5. Please review the data sets approved for the associated paper proposal to ensure that they match the data sets used in the manuscript. Data sets are periodically added to the Dataset Request Form, so we recommend reviewing these to make sure that all applicable data set consent groups have been selected. If any additional data sets approvals are needed, please request these. If any of the data sets approved for the manuscript were not used, please cancel these requests. Note: any TOPMed investigator may request data sets for a proposal, but only the paper proposal submitter or their designee may cancel data sets for a proposal.

Once these steps have been completed, authors can then submit their manuscript and related materials to the TOPMed website, using the manuscript submission form.

Manuscripts should be submitted for review at least 10 business days prior to submission to a journal with the understanding that if anything is missing, approval may take longer than that. To submit a manuscript, use the manuscript submission form. You may save a draft of your upload materials before submitting. To do this, click “save as draft.” You will be able to access your draft from the Dashboard link on the top right corner of the TOPMed webpage. The manuscript drafts and submissions will be listed under the manuscript tab.

  1. You will be required to insert the title, full list of authors, and journal considered for submission.
  2. Choose the paper proposal that is associated with your manuscript. If you begin typing a unique word from your proposal title, a list of proposals to choose from will appear in the drop down menu. The field will autocomplete.
  3. Check the box indicating that the manuscript has been discussed and approved by the Working Group or is single PI.
  4. Upload the signed Working Group convener letter of approval for your manuscript. The manuscript must be approved in writing by the Working Group conveners.  Please review the template for the Working Group approval. If this manuscript is based on a single PI proposal, Working Group approval is not required. Instead of a Working Group approval letter, please upload a note confirming that this is still a single PI manuscript.
  5. Upload all of the manuscript documents. If any of your supplementary files exceed 16 MB, please send them in email to topmed-pubs@westat.com along with the title of your manuscript.
  6. Upload all required study-specific approval documentation. Include PDFs of any approval letters or emails you have received. If any studies have not responded to your request for review within two weeks, please include a list of these studies, noting who you contacted and the date you contacted them. If this manuscript is based on a single PI proposal, this documentation is not required.
  7. Check the box indicating that you have followed the instructions for TOPMed Acknowledgements.
  8. Check the box confirming that the data set approvals for the associated paper proposal match the TOPMed data sets used within this manuscript. Make any needed data set requests or cancellations to ensure that this list of data sets matches what was used in the manuscript.
  9. Check the box indicating that you have followed the Data Use Limitations for each of the data sets checked in the previous step.
  10. If your manuscript does not require data set request and approval, check the box indicating this and describe in the field below why this is the case. This only applies to a small set of manuscripts, such as when only Genomic Summary Results (e.g., association results) from a previously approved manuscript are being used, or for methods papers that do not make direct use of any individual-level phenotypic or genotypic data.
  11. Check the box indicating that you have included at least one co-author representative from each study used in the analysis or the study PI declined an offer to have their study represented. Please review the parent studies that require co-author representation.
  12. Check the box indicating that you have included at least one co-author representative from the ACC, or they declined authorship or deemed acknowledgement sufficient.
  13. Check the box indicating that you have included at least one co-author representative from the IRC, or they declined authorship or deemed acknowledgement sufficient.
  14. Check the box indicating that you have included at least one co-author representative from any relevant omics center(s), or they declined authorship or deemed acknowledgement sufficient.
  15. Check the box indicating that you certify that all co-authors have reviewed and approved the manuscript for submission.

When all of the above steps have been completed, you may submit your manuscript for review by clicking the “submit” button at the bottom of the page. You will receive an email stating that your manuscript has been successfully submitted for administrative and data set review.

Once your manuscript and supporting materials have been successfully uploaded and submitted, the ACC will perform an administrative check. This will include checking for the following: 

You will receive an email stating whether the manuscript has been approved or needs revisions within three business days.

If any of the required items are missing, the submitting author will receive an email from the ACC asking for administrative changes to the manuscript. The submitting author will then need to resubmit the manuscript to the TOPMed website.

If there are no administrative changes necessary, then the PIs (or their appointed Dataset Contacts) of the datasets used in the manuscript will be notified that a manuscript using their data is ready for journal submission. This begins a final review period of seven business days, during which Dataset Contacts have the option to leave comments and mark the manuscript as approved or disapproved.

  • If all Dataset Contacts mark the manuscript as approved, the submitting author will receive an automated approval email from topmed-pubs@westat.com. Authors should still carefully review any comments left by Dataset Contacts and resolve any requests.
  • If a manuscript is marked as disapproved by one or more Dataset Contacts, the submitting author should contact all disapproving study PIs directly to resolve their concerns. The ACC can help determine whether a new TOPMed manuscript submission is needed.
    • If a new submission is needed, follow the steps listed above for manuscript submission, and the ACC will mark the previous disapproved submission as superseded.
    • If a new submission is not needed, the submitting author should alert the ACC at topmed-pubs@westat.com once the study PIs have granted full approval. The ACC will then mark the manuscript submission as “Approved” on the TOPMed website.

Upon receiving approval from all relevant PIs and Dataset Contacts, and completing any necessary study-specific reviews still in progress, the lead authors may submit the manuscript to a journal for peer-review.  

Please notify NHLBI when your manuscript is accepted. Inform the ACC when your manuscript has been published, providing the PubMed ID by emailing to topmed-pubs@westat.com with the information, which will be added to the TOPMed Publication Page.

You may also choose to notify the ACC (topmed-pubs@westat.com) if the paper is posted online as a preprint ahead of 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 data sets are used so we can update our records.