As we begin a new year, let’s look back at the top NCBI Insights Blog posts of 2024 based on number of views.
In case you missed any of these, check them out:
Continue reading “Top of 2024: A Look at the NCBI Insights Blog “
Tag: Database of Genotypes and Phenotypes (dbGaP)
Open Access! Million Veteran Program Genome-Wide PheWAS Results Now Available in dbGaP!
The Million Veteran Program (MVP) is a research program from the U.S. Department of Veterans Affairs (VA) that has collected and analyzed health information from over one million veteran volunteers. The data include genes, lifestyles, military experiences, and exposures that may impact health and wellness.
The results of the MVP phenome-wide association study (PheWAS) analysis are now available in NLM-NCBI’s database of Genotypes and Phenotypes (dbGaP). The PheWAS summary data is based on information from approximately 600,000 veterans from four broad ancestry groups, with hundreds of phenotypic traits recorded in medical records. This is one of the largest publicly available PheWAS datasets to date and does not require an application to access the data. Continue reading “Open Access! Million Veteran Program Genome-Wide PheWAS Results Now Available in dbGaP!”
Using NCBI Resources for Genotype-Based Medication Optimization
NCBI offers a variety of clinical genetic resources to help you research, diagnose, and treat diseases and conditions. You can quickly and easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website.
How and why should you use our resources? Consider the example below.
Your patient is a 58-year-old woman who has been diagnosed with Acute Coronary Syndrome, scheduled for an angioplasty, and she will need to take clopidogrel for at least three months. She mentions that her father died of a stroke while taking the drug and is concerned. You look into pharmacogenetic influences on clopidogrel response and use the results of your patient’s genetic test to determine if a change in the prescription is needed. Continue reading “Using NCBI Resources for Genotype-Based Medication Optimization”
dbGaP: Making it Easier to Find Study Data with Third-Party Annotations
The database of Genotypes and Phenotypes (dbGaP) is a free resource that contains human data from a variety of large-scale studies. While you can’t view individual-level data without applying for controlled access, you can easily find dbGaP studies using the dbGaP Advanced Search (see screenshot below) and quickly filter studies based on study variables, molecular data type, study focus, NIH Institute, study consent, and more. Third-party annotations and mapping of phenotypic and study variables to controlled vocabularies allow you to search across studies. Once you find a study of interest, you can follow the Authorized Access link on records to apply for access.
Phenotypic and study variables include:
- Clinical measures (e.g., height, weight, blood pressure)
- Demographic information (e.g., age, gender, ethnicity)
- Sample information (e.g., analyte type, body site)
- Molecular data type (e.g., DNA sequence, genotypes, gene expression)
Continue reading “dbGaP: Making it Easier to Find Study Data with Third-Party Annotations”
New dbGaP Subject Sample Telemetry Report Now Available
What is it and why does it matter?
The Database of Genotypes and Phenotypes (dbGaP) has been used for over a decade to safely store and provide access to anonymized patient-level data related to research studies. Now you can get a Subject Sample Telemetry Report (SSTR) providing you more details about a dbGaP submission.
With a growing database of over 2,300 studies with billions of demographic, phenotypic, and exposure measurements, we want to ensure you can easily access publicly available information for data submitted to us.
What information is included in this report?
The SSTR is a one-stop shop for: Continue reading “New dbGaP Subject Sample Telemetry Report Now Available”
Submit your data to dbGaP in 3 easy steps!
Do you have human genetic data from a large-scale study? Submit your data to NCBI’s Database of Genotypes and Phenotypes (dbGaP) to contribute to meaningful discoveries about health. dbGaP contains data from more than 2.8 million study participants who have provided over 3.3 million molecular samples.
How do I submit data to dbGaP?
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Step 1: Register your study
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Step 2: Submit your data and get your study accession (phs#)
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Step 3: Release your data
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Continue reading “Submit your data to dbGaP in 3 easy steps!”
dbGaP: Data and analyses from millions of study participants, samples, and trillions of genotypes!
Are you familiar with the well-known Framingham Heart Study, a multi-generation study of residents of Framingham, Massachusetts begun in 1948? Much of what is now known about the impact of genetics, lifestyle, and diet on cardiovascular health and disease has come from this research study. (See PMC4159698 for a historical perspective.) Did you know that data from this study and over 2,000 other studies that demonstrate the relationship between genetic and medical outcomes and other phenotypes are available from NCBI’s Database of Genotypes and Phenotypes (dbGaP)?
dbGaP was established in 2007 as a repository of human data from large scale studies. You can access data from more than 2.8 million study participants who have provided over 3.3 million molecular samples. You can retrieve patient-level phenotypic (e.g., demographic, clinical, exposure) data and molecular (e.g., called genotypes omics, sequence) data, and the results of association analyses from genome-scale case-control and longitudinal studies of heritable diseases.
What types of studies and data are available in dbGaP?
dbGaP contains a wide range of studies and types of data, all relating to human genetic and phenotypic measurements. Most dbGaP data are from NIH-funded research, but recently we have expanded to include non-NIH funded studies. An easy way to find dbGaP Studies, Phenotype and Molecular Datasets, Variables, Analyses and Documents is through the dbGaP Advanced Search (Figure 1). The interface allows you to filter results by different characteristics depending on the tab you choose.
Figure 1. The dbGaP Advanced Search interface. Tabs that appear at the top of the web interface allow you to select the studies, datasets, analyses, etc. of interest. Filters (facets) appear on the left (see inset). Click on filters to select values to find Links on the study summary pages provide direct access to data. Top panel: Studies tab and the corresponding filter categories. Bottom panel: Molecular data tab results with Study (Framingham SHARe), Markerset Source (Affymetrix) filters applied.
Connect with NCBI at ASHG 2022
Join us October 25-29 in Los Angeles, CA
We are looking forward to seeing you in-person at the American Society of Human Genetics (ASHG) annual meeting, October 25-29, 2022, in Los Angeles, California.
We will present a variety of talks and posters featuring our clinical and human genetic resources, as well as genome products and tools. We are excited to introduce the NIH Comparative Genomics Resource (CGR), a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources to biomedical research. If you’re interested in providing feedback that will be used to help drive CGR forward, consider joining our round table discussion.
Check out NCBI’s schedule of activities and events:
Using NCBI resources to research, detect, and treat genetic phenotypes
Clinical Genetics Information at Your Fingertips
NCBI offers a portfolio of medical genetics resources to help you research, diagnose, and treat diseases and conditions. You can easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website. We also encourage you to join our community of thousands of submitters and share your germline and/or somatic data to advance discovery and optimize clinical care.
How and why should you use our resources? Consider the example below.
Your patient is a 40-year-old mother of two presenting with changes in bathroom habits, bleeding, and belly pain. She has a medical history of colonic polyps. Her family history reveals that her maternal grandmother, mother and uncle had several forms of cancers including colon, breast, and endometrium.
Continue reading “Using NCBI resources to research, detect, and treat genetic phenotypes”
Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV
The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The development of GDV led to a few different types of genome browsers along the way, each one originally delivering visual displays for particular datasets. We developed the 1000 Genomes Browser for variation data from the 1000 Genomes project, the dbGaP Data Browser for controlled-access sequence read alignment data, and the GeT-RM browser for Genome in a Bottle (GIAB) data.
The data displayed in these three browsers is now either obsolete and/or can largely be accessed from the GDV browser or other NCBI resources. Moreover, unlike GDV, these older browsers are no longer under active development and the data has not been updated to meet changing needs of the communities they were developed to serve. For these reasons we will retire these browsers in April 2022. Please see details below for more information on the data displayed in these browsers and how to access and display these data now through GDV and other means.