Trans-Omics for Precision Medicine | TOPMed
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What is TOPMed?
Trans-Omics for Precision Medicine (TOPMed), is a program of the National Heart, Lung and Blood Institute (NHLBI), a part of the National Institutes of Health, which aims to improve scientific understanding of the fundamental biological processes that underlie heart, lung, blood, and sleep (HLBS) disorders and advance precision medicine in ways that lead to disease treatments tailored to individuals’ unique genes and environments.
TOPMed supports these scientific advances through the integration of whole-genome sequencing (WGS) and other omics data (e.g., metabolic profiles, epigenomics, protein and RNA expression patterns) with molecular, behavioral, imaging, environmental, and clinical data from pre-existing parent studies that have large samples of human subjects with rich phenotypic characterization and environmental exposure data. TOPMed also collects environmental and behavioral data, such as dietary habits, physical activity, and socioeconomic factors, to provide a more comprehensive understanding of the factors that contribute to these disorders.
Explore the Data
The TOPMed program provides data resources for researchers studying heart, lung, blood, and sleep disorders. These data resources include various types of genomic and other data, such as whole-genome sequencing, whole-exome sequencing, RNA sequencing, epigenetic data, metabolomic data, and proteomic data. Researchers who wish to access TOPMed data, including electronic health records, medical imaging data, and other patient health information, must get approval through the Database of Genotypes and Phenotypes (dbGaP). Once approval is granted, researchers can access the data from NHLBI BioData Catalyst® (BDC) or dbGaP.
BioData Catalyst (BDC)
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Cloud-based computing ecosystem
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Features secure workspaces, tools, applications, and workflows
- Hosts data and supports collaboration
The TOPMed program uses BioData Catalyst (BDC) as a resource to facilitate research efforts. BDC is a cloud-based ecosystem where researchers can access NHLBI datasets, including TOPMed data, and leverage innovative data analysis tools, applications, and workflows to accelerate their research efforts. Additionally, BDC allows researchers to bring their own data, collaborate, and share their findings with other researchers in the community, ultimately driving discovery and scientific advancement in precision medicine.
TOPMed Data Freeze 9
- Variant discovery was initially made on approximately 206,000 samples.
- 781 million single nucleotide variants were identified.
- 62 million short insertion/deletion variants were identified and passed variant quality control (QC).
Note: These variant counts are slightly smaller than the corresponding numbers in data freeze 9 due to omitting sites that show no variation in TOPMed samples. More information about WGS methods can be found by selecting a freeze listed on the Methods page.
OMICS Data Processing & Sources
TOPMed Omics data processing is being performed by several sequencing centers. The program requires that omics data be submitted to dbGaP with thorough documentation of bio-sampling, laboratory methods, and sample provenance. Visit the Methods webpage and scroll to the Standards, Pipelines and Flowcharts for Data Processing section to find available documented omics pipelines specific to omics type and phase. Below is a summary of the approved data sources for each study/cohort name categorized by data type.
| Short Name Sort descending | Study/Cohort Name | Populations | dbGaP ID | WGS | RNA-seq | Methylation | Metabolomics | Proteomics |
|---|---|---|---|---|---|---|---|---|
| THRV | Taiwan Study of Hypertension using Rare Variants | Taiwan Chinese families | 2,170 | |||||
| TOPCHeF | Trans-Omics for Precision Medicine for Congestive Heart Failure | Multi-ancestry | phs002038 | 839 | 776 | |||
| UNID_CM | The Genetic Causes of Unexplained Cardiomyopathies | All ages, newborn to adults | 779 | |||||
| WHI | Women's Health Initiative | Women aged 50-79 years | phs001237 | 11,310 | 2,365 | 4,400 | 4,400 | 1,000 |
| walk_PHaSST | Treatment of Pulmonary Hypertension and Sickle Cell Disease with Sildenafil Therapy | Individuals aged 12-70 years | phs001514 | 437 | ||||
| 196,938 | 64,412 | 81,033 | 82,534 | 34,014 |
Published Papers That Used TOPMed Data
Published papers utilize TOPMed data to address topics related to heart, lung, blood, and sleep disorders.
| Title | Journal Name | Publication Date Sort ascending | PMID |
|---|---|---|---|
| A genome-wide association study of alloimmunization in the TOPMed OMG-SCD cohort identifies a locus on chromosome 12 | Transfusion | 38966903 | |
| Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium | Human Molecular Genetics | 38747556 | |
| Metabolite signatures associated with microRNA miR-143-3p serve as drivers of poor lung function trajectories in childhood asthma | eBioMedicine | 38458111 | |
| Transcriptome-wide association study of the plasma proteome reveals cis and trans regulatory mechanisms underlying complex traits | AJHG | 38320554 | |
| A genetic association study of circulating coagulation Factor VIII and von Willebrand Factor levels | Blood | 38320121 |
Resources for the Scientific Community
TOPMed data are being made available to the scientific community as a series of “data freezes”:
- genotypes and phenotypes via dbGaP
- read alignments via the Sequence Read Archive (SRA)
- variant summary information via the Bravo variant server
- single nucleotide polymorphisms (dbSNP)
TOPMed WGS data are contained in study-specific accessions with names containing “NHLBI TOPMed,” while most phenotypic data are in parent study accessions. The TOPMed accessions can be identified by searching the dbGaP website for “TOPMed.” More information about the available data and how to access it can be found on the Data Access page.
