TOPMed papers require acknowledgements for TOPMed sequencing/omics as well as for study-specific data. Study-specific acknowledgements are specified in the "Acknowledgment Statement" under "Study Attribution" on the "Study" tab of each accession's dbGaP home page and on our Study-specific Acknowledgements page; general TOPMed acknowledgements are described below.
Please use the following template paragraph to acknowledge the use of TOPMed data in publications. It should be located within your main manuscript document.
Molecular data for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). <Insert molecular data type (Genome Sequencing, RNASeq, Metabolomics, Methylomics, Proteomics)> for "NHLBI TOPMed: <insert Parent Study name>" (<insert phs# with version extension)>) was performed at <insert omics/sequencing center name (grant/contract number) from the Table below>. [Repeat this sentence for each TOPMed Study-molecular data type combination as appropriate.] Core support including centralized genomic read mapping and genotype calling, along with variant quality metrics and filtering were provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1; contract HHSN268201800002I). Core support including phenotype harmonization, data management, sample-identity QC, and general program coordination were provided by the TOPMed Data Coordinating Center (R01HL-120393; U01HL-120393; contract HHSN268201800001I). We gratefully acknowledge the studies and participants who provided biological samples and data for TOPMed.
For example, to acknowledge use of TOPMed data from the Framingham Heart Study and the Jackson Heart study (note that here we added a phs# extension “v1.p1” to denote the actual version that was downloaded and used; version numbers vary over time, so are not included in the table below):
Molecular data for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). Genome sequencing for “NHLBI TOPMed: Whole Genome Sequencing and Related Phenotypes in the Framingham Heart Study” (phs000974.v1.p1) was performed at the Broad Institute Genomics Platform (3R01HL092577-06S1, 3U54HG003067-12S2). RNASeq for “NHLBI TOPMed: Whole Genome Sequencing and Related Phenotypes in the Framingham Heart Study” (phs000974.v1.p1)” was performed at the Northwest Genomics Center (HHSN268201600032I). Genome sequencing for “NHLBI TOPMed: The Jackson Heart Study” (phs000964.v1.p1) was performed at the Northwest Genomics Center (HHSN268201100037C). Core support including centralized genomic read mapping and genotype calling, along with variant quality metrics and filtering were provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1; contract HHSN268201800002I). Core support including phenotype harmonization, data management, sample-identity QC, and general program coordination were provided by the TOPMed Data Coordinating Center (R01HL-120393; U01HL-120393; contract HHSN268201800001I). We gratefully acknowledge the studies and participants who provided biological samples and data for TOPMed.
When many studies are involved, we recommend placing NHLBI, IRC, and DCC acknowledgements in the manuscripts’ main acknowledgements section and the study-specific data acknowledgements in a supplementary table or document. An example of this can be seen on the Paper Proposal Resource page for each proposal.
TOPMed Omics Support Table
The following table can be used to generate the sequencing/omics support information for your manuscript, as indicated in the examples above. Please note that authors are strongly encouraged to use the auto-generated version of this table that is provided on each Paper Proposal Resource page, based on the data sets approved for that specific proposal.
To easily find a phs number in the table below, use your browser's built in functionality to search this page (Ctrl-F or Cmd-F on most desktop computers).