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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)

  • Cloud-based computing ecosystem

  • 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.

TOPMed WGS and Omics Summary of Approved Projects
TOPMed WGS and Omics Summary of Approved Data
Short Name Study/Cohort Name Populations dbGaP ID WGS RNA-seq Methylation Metabolomics Proteomics
AA_CAC African American Coronary Artery Calcification project African American families phs002194 1,159
AFGen Identification of Common Genetic Variants for Atrial Fibrillation and PR Interval - Atrial Fibrillation Genetics Consortium European ancestry AFGen dbGaP IDs 12,742
Africa6K Integrative Genomic Studies of Heart and Blood Related Traits in Africans African ancestry phs002194 6,392 2,934
Amish Genetics of Cardiometabolic Health in the Amish Old Order Amish large extended pedigrees phs000956 1,120
ARIC+VTE Venous Thromboembolism project African American (20%) phs001211 phs001402 phs000993 10,531 6,111 16,524 16,524
ATGC Asthma Translational Genomics Collaborative African American, Mexican, and Puerto Rican individuals ATGC dbGaP IDs 16,494 9,290
BAGS Barbados Asthma Genetics Study Barbados families of African descent with >40% of asthmatic members phs001143 1,085
BCC-PREG The Boston-Colombia Collaborative for Adverse Pregnancy Outcomes White, Black, Asian, Hispanic, White Hispanic, AfroCarribean, Ameridians, Mixed Please see this TOPMed Project's Parent Studies. 14,615
BioMe Mount Sinai BioMe Biobank African American (24%), Hispanic/Latino (35%), European (32%), Other (10%) phs001644 11,626
Boston-Brazil_SCD Boston-Brazil Collaborative Study of Sickle Cell Disease Brazilian phs001599 415
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 Sort descending Journal Name Publication Date PMID
Rare Coding Variants Associated With Electrocardiographic Intervals Identify Monogenic Arrhythmia Susceptibility Genes: A Multi-Ancestry Analysis Circulation: Genomic and Precision Medicine 34319147
Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants Nature Communications 33057025
A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data NAR Genom Bioinform 35591888
A common TCN1 loss of function variant is associated with lower vitamin B12 level in African Americans Blood 29764838
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies Nat Methods 36303018

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.

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