Access to comprehensive and accurate allele frequency data is essential to understanding the impact of genetic variations on human health and disease. Allele Frequency Aggregator (ALFA) provides the Database of Single Nucleotide Polymorphisms (dbSNP) with allele frequency data for 200K subjects from the Database of Genotypes and Phenotypes (dbGaP). ALFA adheres to the Findable, Accessible, Interoperable, and Reusable (FAIR) Data Principles providing open access to valuable allele frequency data. Continue reading “Explore Population Genetics in dbSNP with NCBI’s Allele Frequency Aggregator (ALFA)”
Tag: Single Nucleotide Polymorphism Database (dbSNP)
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”
Join NCBI at ASHG 2023
November 1-5 in Washington, D.C.
We look forward to seeing you in person at the American Society for Human Genetics Annual Meeting (ASHG 2023), November 1-5, 2023, in Washington, D.C. We will participate in a variety of activities and events including hosting an exhibit booth where you can stop by to meet NCBI experts, ask questions, provide feedback, or just chat! We’re especially excited to share our recent efforts on our clinical and human genetic resources and provide an update on the NIH Comparative Genomics Resource (CGR).
Check out NCBI’s schedule of activities and events:
dbSNP Enhances Scalability, Data Diversity, and Accessibility
As part of the Human Genome Project, NCBI, part of the National Library of Medicine, and the National Human Genome Research Institute (NHGRI) established the Single Nucleotide Polymorphism database (dbSNP) in 1998. Over the last 25 years, dbSNP has evolved into a reliable central public repository for genetic variation data. dbSNP is a community-accepted reference data set for genetic research, analysis pipelines, and for both open-source and commercial tools. It is also an essential part of genetic research and discovery. For example, dbSNP data are used in nearly all human genetic variation research workflows and it serves as the foundation for commercially available ancestry testing products.
Current dbSNP statistics include:
- 3,800 submitters from all over the world
- 3.3 billion submitted SNP records
- 1.1 billion Reference SNP records
- 1.0 billion Reference SNP records with population frequency
- dbSNP accessions are cited in over 65K publications
Continue reading “dbSNP Enhances Scalability, Data Diversity, and Accessibility”
NCBI ALFA Project at Bio-IT World 2022 Hackathon
Announcing the Allele Frequency Aggregator (ALFA) Project as part of the Bio-IT World 2022 Hackathon: Visualization of NCBI ALFA Variants
Join NCBI at the Bio-IT World 2022 Hackathon on May 4-5, 2022 to learn about and work with data from our ALFA project! The primary goal of this hackathon project is to develop a novel tool, app, or approach to explore and visualize NCBI ALFA variants and allele frequency for 12 different human populations. We aspire to create a new helpful variant interpretation resource for the clinical and research communities.
We hope to see you there! More information and registration here. Continue reading “NCBI ALFA Project at Bio-IT World 2022 Hackathon”
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”
NCBI genome browsers: search and you will find!
If you’ve ever tried searching for a genomic location in NCBI’s Genome Data Viewer (GDV) or Variation Viewer and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as HGVS patterns (e.g. NM_001318787.2:c.2258G>A) and Ensembl IDs. You can also search by chromosome coordinates, cytogenetic band, assembly scaffold/component, disease/phenotype, dbSNP identifier, or RefSeq transcript/protein accession. We’ve gathered example searches in the table below.
Search term | Example(s) |
---|---|
Chromosome coordinate | chr1:1,500,000-2,000,000 chr2: 1.5M-2,540.2K 3: 21.335M..21.337M 3: 21.335M..21.337M chr5 |
Cytogenetic band | 1p36.21 2q13 |
Assembly scaffold | NT_005403.18 NW_021159987.1 |
Assembly component | AC106865.4 AC018680.4 |
Gene/protein name | PTEN protease |
Disease/phenotype | diabetes eye color |
SNP rsID | rs863223352 |
dbVar ID | rs863223352 |
RefSeq transcript/protein accession | NM_017551.3 XP_011538173.1 |
Ensembl gene/transcript indentifier | ENSG00000233258 ENST00000404547 |
HGVS | NM_001318787.2:c.2258G>A NP_001289617: p.Arg272Cys |
When you search by single coordinate, SNP or dbVar ID, or HGVS, the browser view zooms to the location of the search result. A marker is automatically created to identify the searched position. For HGVS, the marker is labelled with the corresponding rsID, if there is one.
![variation viewer search by HGVS results](https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2021/11/variation-viewer-search-by-HGVS-results.png?resize=1024%2C422&ssl=1)
As always, please contact us if you have additional questions or suggestions about this or any other feature in GDV or Variation Viewer. You can use the Feedback button on the page or write to the NCBI Help Desk directly.
View GEO, SRA, or dbGaP data tracks in NCBI’s Genome Data Viewer
Did you know that you can see epigenomic or other experimental data in NCBI’s Genome Data Viewer (GDV)?
You can easily add aligned study results from GEO, SRA, and dbGaP as data tracks to GDV browser view. Just go to the Tracks button on the toolbar and select the menu option to Configure Tracks. Navigate to the ‘Find Tracks’ tab on the pop-up Configure panel (Figure 1).
![screenshot of genome data browser, showing 'Tracks' menu and 'Find Tracks' tab](https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2021/10/image2021-10-12_14-36-44.png?resize=717%2C713&ssl=1)
Continue reading “View GEO, SRA, or dbGaP data tracks in NCBI’s Genome Data Viewer”
NCBI Presents Two Online CoLabs at ASHG 2020!
Two up-and-coming NCBI resources will be featured in videos, surveys and live events at the American Society for Human Genetics (ASHG) 2020 Annual Meeting. Come and watch on-demand videos in the CoLab Theater. Then, let us know what you think and how you do or might use these resources by either taking an online survey or joining us for the CoLab Live! Events on Thursday, October 29, 2020.
Continue reading “NCBI Presents Two Online CoLabs at ASHG 2020!”
dbSNP human build 154 release + ALFA data
dbSNP human build 154, now available, includes new ALFA (Allele Frequency Aggregator) variants and allele frequency. This build contains over two billion Submitted SNP (ss) records and 730 million Reference SNP (rs) records.
New features include:
- dbSNP search now support HGVS and protein variant search
- RefSNP page linked to Litvar information
- Filter and facet to retrieve all SNPs with ALFA frequency
See the release notes for more information about what’s new in build 154.