TOPMed Acknowledgements

Date last changed April 14, 2020

Last updated April 2020

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 (HHSN268201500014C). 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).

TOPMed Accession # TOPMed Study Short Name TOPMed Phase TOPMed Project Omics Center Short Name Omics Support
phs001543 AFLMU 2.4; 2.5 AFGen Broad Genomics 3UM1HG008895-01S2; HHSN268201500014C
phs000956 Amish 1 Amish Broad Genomics 3R01HL121007-01S1
phs001211 ARIC 2 VTE Baylor 3U54HG003273-12S2 / HHSN268201500015C
phs001211 ARIC AFGen 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001435 AustralianFamilialAF 1.5 AFGen Broad Genomics 3U54HG003067-12S2 / 3U54HG003067-13S1
phs001143 BAGS 1 BAGS Illumina 3R01HL104608-04S1
phs001644 BioMe AFGen 2.4 AFGen MGI 3UM1HG008853-01S2
phs001624 BioVU_AF 2.4 AFGen MGI 3UM1HG008853-01S2
phs001624 BioVU_AF 2.4 AFGen Baylor 3UM1HG008898-01S3
phs001599 Boston-Brazil_SCD 2 Boston-Brazil_SCD Baylor HHSN268201500015C
phs001599 Boston-Brazil_SCD 5 Boston-Brazil_SCD Baylor HHSN268201600033I
phs001726 CAMP 3 CRA_CAMP NWGC HHSN268201600032I
phs001612 CARDIA 3 CARDIA Baylor HHSN268201600033I
phs001728 CARE_BADGER 3 ATGC NWGC HHSN268201600032I
phs001729 CARE_CLIC 3 ATGC NWGC HHSN268201600032I
phs001730 CARE_PACT 3 ATGC NWGC HHSN268201600032I
phs001732 CARE_TREXA 3 ATGC NWGC HHSN268201600032I
phs001600 CATHGEN 2.4 AFGen MGI 3UM1HG008853-01S2
phs001600 CATHGEN 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
phs001189 CCAF 1 AFGen Broad Genomics 3R01HL092577-06S1
phs000954 CFS 3.5 CFS NWGC HHSN268201600032I
phs000954 CFS 1 CFS NWGC 3R01HL098433-05S1
phs001602 ChildrensHS_GAP 3 ATGC NWGC HHSN268201600032I
phs001603 ChildrensHS_IGERA 3 ATGC NWGC HHSN268201600032I
phs001604 ChildrensHS_MetaAir 3 ATGC NWGC HHSN268201600032I
phs001605 CHIRAH 3 ATGC NWGC HHSN268201600032I
phs001368 CHS 3 CHS Baylor HHSN268201600033I
phs001368 CHS VTE 2 VTE Baylor 3U54HG003273-12S2 / HHSN268201500015C
phs000951 COPDGene 2.5 COPD Broad Genomics HHSN268201500014C
phs000951 COPDGene 1 COPD NWGC 3R01HL089856-08S1
phs000951 COPDGene 2 COPD Broad Genomics HHSN268201500014C
phs000988 CRA 1 CRA_CAMP NWGC 3R37HL066289-13S1
phs000988 CRA 3 CRA_CAMP NWGC HHSN268201600032I
phs001546 DECAF 1.5 AFGen Broad Genomics 3U54HG003067-12S2 / 3U54HG003067-13S1
phs001412 DHS 2 AA_CAC Broad Genomics HHSN268201500014C
phs001472 ECLIPSE 3 ECLIPSE MGI HHSN268201600037I
phs001606 EGCUT 2.5 AFGen Broad Genomics HHSN268201500014C
phs000946 EOCOPD 1 COPD NWGC 3R01HL089856-08S1
phs000974 FHS 1 FHS Broad Genomics 3U54HG003067-12S2
phs000974 FHS AFGen 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001542 GALAI 3 ATGC NWGC HHSN268201600032I
phs000920 GALAII 1 PGX_Asthma NYGC 3R01HL117004-02S3
phs000920 GALAII ATGC 3 ATGC NWGC HHSN268201600032I
phs001661 GCPD-A 3 ATGC NWGC HHSN268201600032I
phs001547 GENAF 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
phs001218 GeneSTAR legacy GeneSTAR Illumina R01HL112064
phs001218 GeneSTAR 2 GeneSTAR Psomagen 3R01HL112064-04S1
phs001218 GeneSTAR AA_CAC 2 AA_CAC Broad Genomics HHSN268201500014C
phs001345 GENOA 2 HyperGEN_GENOA NWGC 3R01HL055673-18S1
phs001345 GENOA AA_CAC 2 AA_CAC Broad Genomics HHSN268201500014C
phs001217 GenSalt 2 GenSalt Baylor HHSN268201500015C
phs001725 GGAF 2.4 AFGen Baylor 3UM1HG008898-01S3
phs001359 GOLDN 2 GOLDN NWGC 3R01HL104135-04S1
phs001395 HCHS_SOL 3 HCHS_SOL Baylor HHSN268201600033I
phs000993 HVH 1 AFGen Broad Genomics 3R01HL092577-06S1
phs000993 HVH VTE 2 VTE Baylor 3U54HG003273-12S2 / HHSN268201500015C
phs001293 HyperGEN 2 HyperGEN_GENOA NWGC 3R01HL055673-18S1
phs001545 INSPIRE_AF 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
phs001607 IPF 3 IPF MGI HHSN268201600037I
phs000964 JHS 1 JHS NWGC HHSN268201100037C
phs001598 JHU_AF 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
phs001662 LTRC 4 LTRC Broad Genomics HHSN268201600034I
phs001402 Mayo_VTE 2 VTE Baylor 3U54HG003273-12S2 / HHSN268201500015C
phs001416 MESA 2 MESA Broad Genomics 3U54HG003067-13S1
phs001416 MESA AA_CAC 2 AA_CAC Broad Genomics HHSN268201500014C
phs001062 MGH_AF 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001062 MGH_AF 1.4; 1.5; 2.4 AFGen Broad Genomics 3U54HG003067-12S2 / 3U54HG003067-13S1; 3U54HG003067-12S2 / 3U54HG003067-13S1; 3UM1HG008895-01S2
phs001434 miRhythm 1.5 AFGen Broad Genomics 3U54HG003067-12S2 / 3U54HG003067-13S1
phs001515 MLOF 3 MLOF Baylor HHSN268201600033I
phs001515 MLOF 2 MLOF NYGC HHSN268201500016C
phs001544 MPP 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
phs001608 OMG_SCD 2 OMG_SCD Baylor HHSN268201500015C
phs001024 Partners 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001735 PCGC_CHD 4 PCGC_CHD Broad Genomics HHSN268201600034I
phs001466 PharmHU 2 PharmHU Baylor HHSN268201500015C
phs001727 PIMA 3 ATGC NWGC HHSN268201600032I
phs001601 PMBB_AF 2.4 AFGen MGI 3UM1HG008853-01S2
phs001601 PMBB_AF 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
phs001569 PROMIS 4 PROMIS Broad Genomics HHSN268201600034I
phs001569 PROMIS 4.5; 4.6 PROMIS Broad Genomics 3UM1HG008895-03S1
phs001682 PUSH_SCD 2 PUSH_SCD Baylor HHSN268201500015C
phs001468 REDS-III_Brazil 2 REDS-III_Brazil Baylor HHSN268201500015C
phs001215 SAFS 1 SAFS Illumina 3R01HL113323-03S1
phs001215 SAFS legacy SAFS Illumina R01HL113322
phs000921 SAGE 1 PGX_Asthma NYGC 3R01HL117004-02S3
phs000921 SAGE ATGC 3 ATGC NWGC HHSN268201600032I
phs000972 Samoan 1 Samoan NWGC HHSN268201100037C
phs000972 Samoan 2 Samoan NYGC HHSN268201500016C
phs001467 SAPPHIRE_asthma 3 ATGC NWGC HHSN268201600032I
phs001207 Sarcoidosis 3.5 Sarcoidosis NWGC HHSN268201600032I
phs001207 Sarcoidosis 2 Sarcoidosis Baylor 3R01HL113326-04S1
phs001446 SARP 2 SARP NYGC HHSN268201500016C
SCVI 5 SCVI Baylor HHSN268201600033I
phs001927 SPIROMICS 4 SPIROMICS Broad Genomics HHSN268201600034I
phs001387 THRV 2 THRV Baylor 3R01HL111249-04S1 / HHSN26820150015C
TOPCHeF 4 TOPCHeF Broad Genomics HHSN268201600034I
phs001933 UCSF_AF 2.4 AFGen Broad Genomics 3UM1HG008895-01S2
UNID_CM 5 UNID_CM Baylor HHSN268201600033I
phs000997 VAFAR 1.5; 2.4; 5.3 AFGen Broad Genomics 3U54HG003067-12S2 / 3U54HG003067-13S1; 3UM1HG008895-01S2; 3UM1HG008895-01S2
phs000997 VAFAR 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001032 VU_AF 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001514 walk_PHaSST 2 walk_PHaSST Baylor HHSN268201500015C
phs001040 WGHS 1 AFGen Broad Genomics 3R01HL092577-06S1
phs001237 WHI 2 WHI Broad Genomics HHSN268201500014C
  • Broad Genomics = Broad Institute Genomics Platform
  • Baylor = Baylor College of Medicine Human Genome Sequencing Center
  • Illumina = Illumina
  • MGI = McDonnell Genome Institute
  • NWGC = Northwest Genomics Center
  • NYGC = New York Genome Center
  • Psomagen = Psomagen
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