NHLBI TOPMed: Omics Phenotypes of Heart, Lung, and Blood Disorders (X01)

FAQs: Frequently Asked Questions

Overview:

This Funding Opportunity Announcement (FOA) invites applications for access to NHLBI-funded capacity for genome-wide high throughput assays for investigators wishing to study the genetic basis and omics signatures of common, complex heart, lung, and blood disorders. Successful applicants will provide biospecimens and receive whole genome sequence or other omics data. No funding will be provided for specimen preparation or data analysis. Successful applicants will also be required to deposit phenotypic data associated with their biospecimens in a public database such as database of Genotypes and Phenotypes(dbGaP) or NHLBI BioData Catalyst (BDC).

Last updated August 15, 2025.

Please re-check this page periodically, as new questions and answers will continue to be added as applicable.

Omics Questions for the X01 FAQ

  1. Can I propose a large scale whole genome sequencing project to TOPMed?
    After completing whole genome sequencing of over 200,000 DNA samples, TOPMed has covered many major cohorts of studies in heart, lung, blood, and sleep diseases. Applicants interested in WGS projects should check existing studies in TOPMed website (https://topmed.nhlbi.nih.gov/), progress report on WGS (https://nhlbi.sph.umich.edu/report/) and consult NHLBI staff about the novelty and feasibility of their applications prior to submission.
     
  2. Can I propose trans-omics (transcriptome, methylome, proteome, and metabolome) measurements on thousands of subjects?
    Applicants need to provide strong rationale for why each omics-measurement is needed to answer their specific scientific questions relevant to NHLBI’s mission and how the sample size is calculated to meet the need and value to existing TOPMed data resource (https://topmed.nhlbi.nih.gov/ and https://nhlbi.sph.umich.edu/omics/). Applicants are strongly encouraged to discuss the feasibility of their applications with NHLBI staff.
     
  3. Can I just propose other omics without WGS data in my application?
    In general, we will provide omics measurements only on samples that have or will have WGS data. Please contact NHLBI staff if you have a special case for consideration.
     
  4. What are the omics that can currently be requested by X01 Investigators?
    They are Whole Genome Sequencing (WGS), Long Read WGS, Epigenetics (methylation), RNA-seq, Metabolomics, Proteomics, and Single-cell omics.
     
  5. Are there any requirements for previous omics being included for an application?
    No, but the applicant should note previous technologies that could indicate sample quality, e.g., array-based genotyping or Whole Exome Sequencing to indicate DNA quality, etc.
     
  6. Is there a minimal requirement for prior omics analysis?
    No. However, if the application includes WGS or other omics data generated elsewhere, investigators may need to address whether the existing data can be part of TOPMed in terms of data sharing, quality, and formats.
     
  7. What are the sample amounts for each current omic platform (new platforms may be introduced in the near future)?
    • Long read WGS, 10 ug high molecular weight DNA for 25-30X coverage is requested. Extraction methods which limit DNA damage are suggested (recommended methods can be shared upon request)
    • WGS, for 20-30X coverage – PCR free preferred unless there is a specific reason for its use.  Minimum concentration: 7ng/uL, minimum volume: 20uL, minimum total amount: 500ng; Preferred concentration: 20+ng/uL, preferred volume: 50uL, preferred total amount: 1ug.
    • Epigenetics (Infinium® MethylationEPIC v2 930K BeadChip.) 1,000 ng of genomic DNA with at least 10ng/uL in concentration for bisulfite array profiling.
    • RNA-seq (50-75 million read pairs, 2x150 bp) – 1,000 ng RNA or more, RIN Score of 7 or better, indicate isolation method (including use of PAXGENE tubes if available) and sample source (e.g. whole blood, tissue, etc.)
    • Metabolomics (mass spectrometry) – 200 microliters for untargeted panel. EDTA plasma or serum is recommended. Applicants should provide a list of specific metabolites that would be required for targeted analysis.
    • Proteomics (Olink) – 50 microliters (25 microliters minimum) EDTA plasma and serum is recommended.
    • Single cell, single nucleus, and spatial assays are available.  Matured technologies are preferred.
    • General data processing methods https://topmed.nhlbi.nih.gov/data-resources/methods
       
  8. Where will the assays be performed?
    Details about the data generation centers will be provided after awards are made. A list of previously awarded centers can be found at TOPMed website (https://topmed.nhlbi.nih.gov/).
     
  9. Is it possible to communicate with the centers that will be performing the assays and QC so we can include that information in the X01 application in order to provide a compelling scenario for our later request for data analysis funds?
    No, as contracted vendors will not be selected before the selection of X01 applications each year.
     
  10. When will data generated be shared with the scientific community?
    All cleaned omics data will be made available to the scientific community. The data cleaning process may take about 6 months after the data become available.  Investigators who submitted biospecimens will participate data cleaning process and receive a copy of the data directly from the labs.
     
  11. Will TOPMed be able to provide a letter of support for the awarded X01 recipient to include in their R01 applications?
    No, TOPMed will not provide a letter of support. However, investigators may include the notification of their X01 awards from NHLBI TOPMed program in their grant/contract applications.
     
  12. Can investigators reference the data of other existing or on-going TOPMed projects as part of their X01 applications in order to increase the sample size for data analysis?
    Yes. NHLBI strongly encourages applicants to leverage existing TOPMed data in their research. Study descriptions can be obtained at https://topmed.nhlbi.nih.gov/ and https://nhlbi.sph.umich.edu/omics/ ). All TOPMed data will be made available to the scientific community through the database of Genotypes and Phenotypes (dbGaP), BioData Catalyst(BDC), or an approved NIH data warehouse.
     
  13. If there are no funds available for the institution, then what does go into the budget forms?
    Award Budget - Not applicable. Funds are not awarded via this X01 resource access award. For Total Federal Funds Requested: Enter $0. Total Federal & Non-Federal Funds: $0. Applicants may contact program officers discussing about other funding mechanisms.