Summary of TOPMed Multi-omics Data

1. Proteomics: Olink
   • ~5400 proteins via multiplex immunoassays

2. Metabolomics: Metabolon
   • 9000 metabolites (~1000 targeted)

3. Methylomics (DNA methylation): Illumina
   • 935,000 methylated DNA sites

Population: CHS Participants with TOPMed WGS (n=4848)

• With permission for genetic studies of primary aims (CVD and aging)
• Without restriction for use by non-CHS investigators

CHS participants have 1-4 measures across years.

Number of measures by CHS year

* measures designated as Y5 may have come from samples collected Y5, Y6, or Y7; those designated as Y9 may have come from Y9 or Y10

Steps To Access TOPMed Omics Data:

Data may be accessed via dbGaP independently of CHS or the TOPMed program. However, there are many advantages to accessing data via CHS (CHS-only analyses) or via TOPMed. These include earlier access to data, jointly-called genotypes, access to the TOPMed Exchange area, etc.

1. CHS-only analyses

         Proposals

• Share proposed analyses with the CHS Omics WG (typically a short presentation at the twice-monthly meeting). Contact: Josh Bis (joshbis@uw.edu)

• Submit a single study proposal via the TOPMed website (must be a TOPMed member) for review by TOPMed (no separate CHS paper proposal required). Details on the TOPMed proposal process can be found by reviewing the TOPMed Publications Policy.
• Select CHS datasets via the TOPMed website – this triggers the process to obtain approval by the CHS PI (Dr. Psaty).

         Datasets

• Request data from the Coordinating Center via the usual process or access via TOPMed. (Note: The CC will not be providing "boutique" data preparation of omics file -- e.g., "selected metabolites", "curated proteins", subsets by phenotype, etc.)
• Users of the data should expect to do some QC and share their findings with the Omics WG.

         Publications

• Submit pen drafts to CHS as a "non-standard" submission via the TOPMed Omnibus in which the lead author serves as the first reviewer.
• Report progress/abstracts/manuscripts to TOPMed via the TOPMed website.

2. Multi-study analyses

          Proposals

• Submit a multi-study proposal via the TOPMed website (must be a TOPMed member) and gain approval through the appropriate TOPMed working group (no separate CHS paper proposal required). Details on the TOPMed proposal process can be found by reviewing the TOPMed Publications Policy.
• Select study datasets via the TOPMed website – each selected study must be approved by the study PI.
• Investigators are encouraged to share proposed analyses with the CHS Omics WG (typically a short presentation at the bi-monthly meeting). Contact: Josh Bis (joshbis@uw.edu)

         Datasets

• Access data for the multiple studies through TOPMed’s exchange area, dbGaP, or on BioData Catalyst.
• Users of the data should expect to do some QC and share their findings with the Omics WG.

         Publications

• Submit pen drafts to CHS as a "non-standard" submission via the TOPMed Omnibus in which the lead author serves as the first reviewer.
• Report progress/abstracts/manuscripts to TOPMed via the TOPMed website.