Tag: Single Nucleotide Polymorphism Database (dbSNP)
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:
See the release notes for more information about what’s new in build 154.
On Wednesday, April 22, 2020 at 12 PM, join NCBI staff to learn how results from the Allele Frequency Aggregator (ALFA) project will help you interpret the biological impact of common and rare sequence variants. ALFA’s initial release includes analysis of genotype data from ~100K unrestricted dbGaP subjects and provides high-quality allele frequency data now displayed on relevant dbSNP records. In this webinar, you will learn about the data in the recent ALFA release, see how to access the data from the web, FTP, and how to programmatically retrieve data by positions, genes, and other attributes using E-utilities and Variation Services API in Python.
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
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.
Figure 1. ALFA allele frequencies for a variant (rs4988235) in the promotor of the lactase gene showing frequency differences across populations.
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
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”
On Wednesday, December 4, 2019 at 12 PM, NCBI staff will present a webinar on the population variation datasets at NCBI such as 1000 Genomes, ExAC, GnomAD, and TopMed that are currently included on dbSNP records. You will learn how to find the data, and how you can used this information to interpret and prioritize variants for further study. You will also see a preview a new initiative, the dbGaP Allele Frequency Aggregator (ALFA), that is based on more than 150,000 subjects in 60 dbGaP studies.
Continue reading “December 4 Webinar: Human population genetic variation data at NCBI”
dbSNP was established in August 1999 as a collaboration between NCBI and the National Human Genome Research Institute (NHGRI) as a database of small scale nucleotide variants. The database includes both common and rare single-base nucleotide variation (SNV), short (=< 50bp) deletion/insertion polymorphisms, and other classes of small genetic variations.
Have you ever searched for a variant in ClinVar with a gene symbol and a c., and wondered why you got no result? Is the variant not in ClinVar, or was something wrong with your search?
Wonder no more – we’ve improved searching in ClinVar so you get results for a gene symbol and c. more often!
While a gene symbol and c. make an ambiguous query and a full HGVS expression is always the best search term, this new service will help you find the variant when gene symbol and c. are all the information that you have.
If you’ve been searching in ClinVar, you might have noticed search improvements introduced in December that reliably connect you with information on your variant of interest. ClinVar has broadened its search capability to accept many different ways of expressing the same variation, including variation described on RefSeq transcripts and proteins. If your variant expression is not reported in ClinVar, we alert you to other variants at the same genomic location or link you to related information in other NCBI resources such as dbSNP, LitVar, and PubMed. ClinVar will also now interpret expressions that contain minor errors or warn you about improper syntax that it cannot interpret.
Figure 1. Improved search results in Clinvar showing mapping of an HGVS expression to the equivalent variant in ClinVar.
Here are some example queries that show the improved search results.
NM_001318787.1:c.2258G>A – an HGVS expression that is not in ClinVar, but ClinVar has an alternate expression for a variant (Figure 1).
NM_004958.3:c.7365C>A – a variant not in ClinVar, but another variant is at the same genomic location is in ClinVar.
NM_002113.2:c.19delG – a variant is not in ClinVar, but there is additional information for the variant in other databases.
We welcome your feedback on your search experience and any additional ideas on how to improve searching in ClinVar.
Join us on Wednesday, February, 2019, when NCBI staff will show you how to use a new set of NCBI variation services that rely on a variant data model called SPDI (Sequence Position Deletion Insertion). These services and data model allow you to inter-convert, map and disambiguate variants in standard formats (RefSNP accessions, HGVS and VCF). Unlike many current variant notation systems, SPDI provides unambiguous, machine-readable definitions of variants. SPDI not only powers SNP build and mapping procedures at NCBI but also our variant sensors that are active in the global search and ClinVar. These services and notation system provide valuable new tools for people who work with sequence variants.additional variant information.
Date and time: Wed, Feb 6, 2019 12:00 PM – 12:30 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
dbSNP build 152 is a small incremental update from build 151 provided for you to begin testing and integrating the new build products into your workflow. Build 152 uses the new system with SPDI variant notation and is now available on FTP and the new RefSNP webpage.
The release notes have more information about what’s new in build 152. If you have any questions or comments, send us an email.