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TOPMed

Centers

The TOPMed program is comprised of centers funded and led by the NHLBI. These centers work in close coordination to support the generation of large-scale genomic data and resources, facilitate publications, and assist TOPMed Research Community which includes over 1,400 investigators and their 42 phenotype-focused working groups and 10 committees.

Administrative Coordinating Center

Westat, Inc. serves as the Administrative Coordinating Center (ACC) for TOPMed. The ACC works in close coordination with people and groups in the TOPMed community, such as TOPMed investigators, the Informatics Research Center (IRC), the sequencing centers, the BDC management core (DMC), and staff from NHLBI.

The ACC supports the TOPMed program by providing:

  • Program administration, coordination, and communication across TOPMed committees and working groups;
  • Scientific consultation and technical assistance to investigators accessing TOPMed data;
  • Publication coordination and tracking, from proposal development through scientific and administrative reviews and publication;
  • Development of a comprehensive Manual of Operations (MOO);
  • Management of the TOPMed website.

National Heart, Lung, and Blood Institute

TOPMed is a program of the National Heart, Lung, and Blood Institute (NHLBI), part of the National Institutes of Health (NIH). The TOPMed Program was established to generate large-scale genomic data resources that enable investigators to improve the understanding of heart, lung, blood, and sleep disorders and advance precision medicine.

The TOPMed program is one part of NHLBI's data science effort, which also includes the NHLBI BioData Catalyst® (BDC) ecosystem. BDC provides tools, applications, and workflows in secure workspaces to analyze TOPMed and other BDC-hosted data. An important goal of BDC is to support the storage, sharing, and analysis of TOPMed data. In turn, TOPMed serves as a key driver for BDC, providing data, tools, users, and use cases to the ecosystem.

The TOPMed program, as part of the NHLBI, works in collaboration with the National Center for Biotechnology Information (NCBI) to share TOPMed-generated data via controlled access in the database of Genotypes and Phenotypes (dbGaP).

Informatics Research Center

The Informatics Research Center (IRC) provides assistance to participating studies, sequencing centers and staff at the NHLBI on the handling, processing and interpretation of large-scale sequence data. The IRC jointly analyzes sequence data and aids study investigators with informatics challenges, particularly for cross-study analyses. Upon learning from NHLBI about newly approved studies, the IRC also sends unique sample identifiers to study investigators, who then assign the unique sample identifiers to their selected samples. A key goal of the Informatics Research Center is to make study results easily accessible to a broad range of scientists.

Resources

 

External Expert Panel

 Among the responsibilities of the External Expert Panel (EEP), foremost is safeguarding the interests and confidentiality of study participants and ensuring their data use limitations are respected.

The EEP is asked to make recommendations, as appropriate, to the NHLBI about:
 

  • Strategies to bring together genomic and other omic characterizations in large numbers of subjects to drive biological insights;
  • Methods to integrate omic data which may provide a multi-dimensional biological view of the disease pathogenesis;
  • Other extant NIH or public resources that could be integrated or leveraged to extend the value or power of the TOPMed study;
  • The design and choice of follow-up functional studies to elucidate important observations from association analysis;
  • Strategic partnerships to realize advances toward the goals of precision medicine;
  • Ethical, Legal, and Social Issues (ELSI) such as return of results to study subjects from this research effort; or
  • Provide feedback on gaps and/or weaknesses in current program strategies.

 

Ethical, Legal, and Social Issues Committee

The ELSI (Ethical, Legal, and Social Issues) Committee moderates discussion of matters regarding access to and use of TOPMed data. The Committee has considered consent, participant privacy, and implementation issues regarding: (1) public sharing of variant summary data in the TOPMed variant server (BRAVO, see URLs); (2) public access to use of a TOPMed reference panel in a genotype imputation server (without sharing individual-level data); (3) sharing detailed information about variants of interest with outside investigators for follow-up studies; and (4) return of results to study participants.

Summary reports prepared by the ELSI Committee contain points for study investigators to consider in making decisions about each issue. These reports are provided below, listed by topic and date:
 

 

Sequencing Centers

TOPMed sequencing centers support study investigators of newly approved TOPMed studies by providing information and supplies for the submission of biospecimens. The sequencing centers learn from NHLBI of newly approved studies and provide those study investigators the requirements for processing biospecimens, barcoded laboratory tubes or plates, and a sample manifest. The study researchers must link the barcode, the unique sample identifier (provided by the IRC), and the local sample identifier together before sending the completed manifest to the sequencing center.

Once the manifest is received, reviewed, and approved, the sequencing center notifies the study investigators to send the samples. When the sequencing center receives specimens, it processes them and sends the raw data to the IRC.

The program requires that omics data be submitted to dbGaP with documentation of bio-sampling, laboratory methods, and sample provenance.

Current sequencing centers:

  • Baylor College of Medicine Human Genome Sequencing Center: Whole Genome Sequencing
  • Baylor-UTHealth Metabolomics Center: Metabolomics
  • Broad Institute and Beth Israel Metabolomics Platform: Metabolomics
  • Broad Institute and Beth Israel Proteomics Platform: Proteomics
  • Broad Institute Genomics Platform: Whole Genome Sequencing, RNA-Seq
  • Cedars-Sinai
  • Illumina: Whole Genome Sequencing
  • Keck Molecular Genomics Core Facility: Methylomics
  • Leland Stanford Junior University
  • McDonnell Genome Institute: Whole Genome Sequencing
  • New York Genome Center Genomics: Whole Genome Sequencing
  • New York Genome Center RNA-seq: RNA-Seq
  • Northwest Genomics Center: Whole Genome Sequencing, RNA-Seq, Methylomics
  • Psomagen: Whole Genome Sequencing
  • University of California San Diego
  • University of Washington
  • Vanderbilt University Medical Center

 

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