Tag: Variation Viewer

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 — **Figure 1.** Variation Viewer showing results of search by an HGVS pattern, NP_001289617.1: p.Arg272Cys.

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.

ClinVar annotations now available in NCBI Genome Browsers

Do you need to know which of the many NCBI dbSNP variants annotated near your region of interest are likely to be functionally or clinically significant? Figure it out with the track labelled ‘ClinVar variants with precise endpoints’, available on sequence display viewers at NCBI, including the Genome Data Viewer (GDV) and Variation Viewer!

This track shows variation annotation, including single nucleotide variants and other short variants (e.g. insertions, deletions, etc.) in the NCBI ClinVar database and provides pathogenicity and other metadata. The ClinVar track is displayed next to the default NCBI and Ensembl gene annotation tracks and other NCBI-provided dbSNP and RNA-seq expression tracks.

screenshot of Genome Data Viewer with 'ClinVar variants' track displayed — **Figure 1.** GDV showing ‘ClinVar variants with precise endpoints’ track next to NCBI human gene annotation. Tracks are color coded for quick and easy interpretation. Legend is also provided.

Continue reading “ClinVar annotations now available in NCBI Genome Browsers” →

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 “dbSNP celebrates 20 years!” →

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.

NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources

As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.

This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!

Continue reading “NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources” →