Tag: dbGaP Allele Frequency Aggregator (ALFA)

Explore Population Genetics in dbSNP with NCBI’s Allele Frequency Aggregator (ALFA)

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)” →

NCBI Posters at the Biology of Genomes Meeting

May 10-14, 2022

We are looking forward to the Biology of Genomes meeting, which will focus on “DNA sequence variation and its role in molecular evolution, population genetics and complex diseases, comparative genomics, large-scale studies of gene and protein expression, and genomic approaches to ecological systems.”

NCBI will present three posters to highlight our Comparative Genomics Resource (CGR) and the Allele Frequency Aggregator (ALFA):

The NIH Comparative Genomics Resource: Amplifying the biology of genomes presented by Valerie Schneider, PhD

On behalf of NIH, NLM is developing the NIH Comparative Genomics Resource (CGR) at NCBI to facilitate organism-spanning data connections and promote new research discoveries. This initiative aims to connect NCBI genomics-associated data types and tools with resources external to NCBI to provide a foundation for reliable comparative analysis for all eukaryotic research organisms. Continue reading “NCBI Posters at the Biology of Genomes Meeting” →

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” →

Allele Frequency Aggregator (ALFA) Release 2 is available!

We are excited to announce the NCBI Allele Frequency Aggregator (ALFA) Release 2 (version 20201027095038) as one of the largest and most comprehensive aggregated variant datasets with allele frequency available as open-access. This release contains 79 dbGaP studies that included 192 thousand subjects and 5.8 trillion combined genotypes that generated allele frequency for 904 million variants with 316 million novel ones, previously unknown in dbSNP (Build 154).

Continue reading “Allele Frequency Aggregator (ALFA) Release 2 is available!” →

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.

The ALFA dataset: New aggregated allele frequency from dbGaP and dbSNP now available

NIH’s data sharing policy now allows unrestricted access to genomic summary results for data from NCBI’s Database of Genotypes and Phenotypes (dbGaP). Pooled allele frequency data from dbSNP and the dbGaP summary results are available as the new Allele Frequency Aggregator (ALFA) dataset. The ALFA dataset includes aggregated and harmonized array chip genotyping, exome, and genome sequencing data. The ALFA data are open access and freely available for you to incorporate into your workflows and applications from the dbSNP web pages (Figure 1), through FTP,and the Variation Services API. dbGaP currently has data for more than 2 million study subjects, approximately 1 million of whom have genotype data that is suitable for input into the ALFA dataset. The first release of ALFA contains data on about 100,000 subjects, and we hope to complete processing of data on the other 925,000 subjects within the next year. This volume and variety of data promises unprecedented opportunities to identify genetic factors that influence health and disease. Register to attend our April 22 webinar and read on to learn more.

ALFA Figure 1. ALFA allele frequencies for a variant (rs4988235) in the promotor of the lactase gene showing frequency differences across populations.

Continue reading “The ALFA dataset: New aggregated allele frequency from dbGaP and dbSNP now available” →

NCBI on YouTube: Get the most out of NCBI resources with these videos

Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.

Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips

This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.

Continue reading “NCBI on YouTube: Get the most out of NCBI resources with these videos” →