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

December 4 Webinar: Human population genetic variation data at NCBI


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.

  • Date and time: Wed, Dec 4, 2019 12:00 PM – 12:45 PM EDT
  • Register

Continue reading

dbSNP celebrates 20 years!


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.

Continue reading

Get “Gene+c.” results in ClinVar


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.

Continue reading

Improved ClinVar search quickly connects you to information about variants


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.

sensor2Figure 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.

February 6 Webinar: New Variation Services for Normalizing, Remapping, and Annotating Variants


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

Register

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 uses SPDI variant notation


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.

November 14 Webinar: Variant Interpretation using NCBI Resources


Next Wednesday, November 14, 2018, NCBI staff will show you how to use NCBI’s genome browsers and other resources to interpret variants. The graphical displays of Genome Data Viewer (GDV) and Variation Viewer offer an interactive experience that allows you to explore NCBI’s rich collection of annotations, datasets and literature for deciphering your variant-associated data. In this presentation, we’ll step through case studies and show you how to quickly display relevant NCBI track sets — including the new RefSeq Functional Elements track, upload a file or remotely-hosted dataset and display these as a track, and use browser tracks to identify known variants, then assess variant functional and clinical significance and allele frequency. You will also learn how to navigate from the browsers to NCBI resources such as ClinVar, dbSNP and PubMed, for additional variant information.

Date and time: Wed, Nov 14, 2018 12:00 PM – 12:45 PM EDT

Register

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.

 

 

See how dbSNP improves data quality at ASHG 2018


NCBI staff will share knowledge on various topics at the American Society of Human Genetics (ASHG) conference this month  in San Diego. Here, on NCBI Insights, we feature some preliminary details for one of NCBI’s dbSNP posters.

You can visit poster 1692W “Improving dbSNP Data Quality and Annotation for Variant Interpretation” on Wednesday, Oct. 17 from 3 PM to 4 PM at ASHG.

Continue reading

Standalone variation services replace Variation Reporter


As of July 2018, a new set of standalone variation services replaces the variant matching functions of Variation Reporter. Variation Reporter was a tool designed to search human sequence variation data by location and to report matching variants found in dbSNP, dbVar, and ClinVar.

The new services are faster, better at handling variants in repeat regions, and scalable to accommodate the continued explosive growth of variation volume. You can find more information about the services in the initial blog post and online SPDI document.

If you would like to report any issues related to these new services and/or would like to provide comments, please write to snp-admin@ncbi.nlm.nih.gov.

If you have any specific questions about the NCBI site in general, contact us at info@ncbi.nlm.nih.gov.

We appreciate your continued support and interaction with the NCBI tools.