The Variation Viewer allows you to view, search, and navigate variations present in dbSNP,
dbVar, and ClinVar in a genomic context. In this video, I will demonstrate the basic functions
of the viewer; and in subsequent videos we will cover more advanced features, such as
adding your own data.
The viewer has 5 general components; search, the gene and exon navigator, sequence viewer,
variant table, and variant filter. I'll start with the Search function. Notice that
you can choose between the current human assembly, GRCh38, and the previous assembly, GRCh37.p13.
To see what search formats are accepted, mouse over the Search component, then click on Search examples.
You can input gene symbol, phenotypes annotated in our Gene database, variant IDs from dbSNP
and dbVar, cytogenetic band, and chromosomal coordinates.
I'll search with the breast cancer gene symbol, BRCA1. Results are shown in two tabs, Genes
and Other features. To update the other components, mouse over the desired gene result and click
on the arrow to the right.
The sequence viewer now displays a Genes track, centered on BRCA1, and three other tracks,
ClinVar Short Variations, ClinVar Large Variations, which are structural variants from dbVar,
and dbSNP. Many other tracks and settings are available in the Configure menu. The sequence
viewer allows you to zoom, pan, move tracks, etc. For more help, go to the Sequence Viewer
documentation page via this Help link.
I'll spend the next couple minutes demonstrating some of the navigation and view capabilities.
Different gene regions can be viewed using options in the gene navigator. For example,
you can limit the view to the boundaries of the current gene by selecting the Region menu
and clicking Go to gene only (no pad). You can switch between genes in the displayed
region using the Gene menu, and depending on your zoom level, you can also switch between
transcripts.
Within the exon navigator, mousing over a circle shows the location of that exon in
the sequence viewer and displays the exon coordinates. Then when you click a circle,
the viewer zooms to that exon and you can now mouse over individual ClinVar and dbSNP
objects. You can zoom all the way to the sequence level using either the slider or this ATG icon.
While we're here in the Sequence viewer, a nice feature is the ability to set a marker
and get the coordinates in genomic, transcript and coding numbering systems, including HGVS.
Of course, I can do this for a known SNP, but also for any position. I'll right-click
on this G, set a new marker, change the name and color if I like, then mouse-over the marker
and select Marker details. You can also download this table for import into a spreadsheet.
To get back to the whole gene display, use the 'Region' options. Notice that as you
change the region displayed, all components, including the Variant Table, automatically
update to show records in the new sequence range.
The Variant table provides these data, and the rows are sorted by location and can be
expanded by clicking on the triangle to reveal allele information from ClinVar.
To the left of the variant table is the Filter component. Check the boxes for the variants
you want displayed.
Finally, to download the selected data in XML format, use this Download link.
For additional information about the Variation Viewer, follow the FAQ and Help links. [point
to links]