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Genome Data Viewer for Human Variation

Topics:

  • Overview of GDV
    • Home page & browser
  • Example #1 (TUBA1A-associated neurological disorders)
    • Demonstration & "Do It Yourself" (DIY) Tasks
  • Example #2 (Dubowitz syndrome and HDAC8) - available in slide deck
    • "Do It Yourself" Tasks

Full material from this workshop is available here: 
View recording and description
View Handout
View Slides

Overview of GDV

Let's go to the GDV home page: 


Once you've selected your organism, you can use the "Search in genome" box to search for genes, chromosomal coordinates, RefSeq accessions, even phenotypes, and the search will lead you into the GDV browser.

Search terms you can use

I'll search with a RefSeq transcript accession, NM_001302688. The result is a link that takes you into the GDV browser focused on the APOE gene.

Search with NM_001302688, click on APOE gene link

The GDV browser has several components. Let's review them: 

GDV browser components

The Sequence Viewer is the main component. You may recognize the viewer as part of other NCBI resources, such as Gene and the Graphics view of GenBank sequence records.
Unique to the GDV browser is the Exon Navigator, just above the Sequence Viewer.
Above the Exon Navigator is a chromosome ideogram with browser navigation functions.
The left side of the page, which is collapsable, has another Search assembly box, and several functions loosely called Widgets, including the ability to add user data, track hubs, and results from BLAST searches.

See the GDV Help documentation, and this link to the Sequence Viewer Legend.

Example #1

This example analysis comes from an article titled, "The mutational and phenotypic spectrum of TUBA1A-associated tubulinopathy", which describes de novo missense variants associated with developmental delay in humans.

 

Image of article title and part of Abstract

 

Here is information from the article that is relevant to our example:
  • Purported novel variant:  c.1307G>A
  • Previously described variants:  c.518C>T and c.641G>A
  • All variants are mapped to transcript NM_006009.3 on GRCh37, "based on HGVS recommendations".
You can review HGVS (Human Genome Variation Society) nomenclature at, http://varnomen.hgvs.org/

 

Image of the HGVS web site home page

Example #1 Tasks:
    1. Is c.1307G>A still a novel variant?
      • Review the refSNP (rs) record
      • Add the ClinVar track in the GDV browser
    2. Locate in GDV previously described variants from the article
    3. Add other sources off data (tracks) in the GDV browser
Example #1, Task 1 (DIY):

Search on the GDV home page (human), with the term: "NM_006009.3:c.1307G>A". 
That search should take you into the browser for chromosome 12, with a marker set on variant, rs1565626851.
Image of GDV browser showing the result of the search with NM_006009.3:c.1307G>A

You can explore the refSNP and ClinVar records by mousing over rs1565626851 in the browser and following links in the popup.

Image of GDV browser showing the popup after mousing over rs1565626851

You can add the ClinVar track in the browser with the Tracks pull-down menu. Go to Tracks / Configure Tracks, then either use the Find Tracks tab to search for ClinVar, or look for the track "ClinVar variants with precise endpoints" and select that track, then click "Configure."

Image of the Tracks - Configure Tracks menu

Image of the ClinVar track added to the view of the marker for rs1565626851

Example #1, Task 2 (DIY):

Locate a previously described variant in GDV, and add other sources (tracks) of data.

Use Task 1 as a guide to locate either c.518C>T  or  c.641G>A. Remember, these are mapped to NM_006009.3.

Image of the results of searching GDV with NM_006009.3:c.518C>T

Note the existence of a known SNP at this position. You might explore other Variation tracks such as, Common Variations, Rare Variations, etc., to see what those tracks provide.

Example #1, Task 3 (DIY):Add other sources of data (tracks) in the GDV browser. For example, add the track hub containing ALFA, the Allele Frequency Aggregator; see https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/.
On the above page, look for the link "Track hub", https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/#track-hub.

Image of the ALFA tracks in the GDV for the TUBA1A example. The position at rs697624 is indicated.

See https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/latest/hg38/ALFA.html for an explanation of the population names and a color legend.

 

 

Last Reviewed: August 4, 2024