Table of Contents : Managing variants : Entering Variants | Variants annotations | Importing variants | Exporting & reporting variants

Entering Variants

Alamut® Visual allows you to annotate and store variants handled through the software.

Alamut® Visual allows you to define several variant folders and to easily switch from one to another. Alamut® Visual enables also to list and navigate easily through all internal variants for the current gene (menu 'Variants' > 'View internal variant List') or for any gene (menu 'Variants' > 'View all internal variants').

Variant annotations can be exported and reported to customizable external files and reports (see Exporting & Reporting) but also be imported from external files (see Importing Variants).

Where and how variants are stored

The basic variant database functionality implementation relies on files stored either on each user's computer, or on a shared file system.
Variants are stored in local variant files, inside a folder that can be specified in the Options dialog box (menu 'Tools' > 'Options' > 'Preferences' tab). By default, this folder is 'AlamutFiles' (inside 'My Documents' on Windows XP or Windows 7, inside 'Documents' on Windows Vista, and inside the user's home folder on Mac and Linux):

Alamut® Visual creates individual variant files per gene, named after the gene's official symbol and with extension 'mut' (e.g. MLH1.mut for MLH1 variants and DMD.mut for DMD variants).

It is also possible to define a set of different folders for variant files (menu 'Folders' > 'Variants').
These folders can be used for different use cases or projects and the menu enables to easily switch from one folder to another:

When switching to another folder, the only visible variants are those that are stored in a file within the selected folder, if any.
The first listed folder shortcut in the menu is always the one that has been defined in the Options dialog box (menu 'Tools' > 'Options' > 'Preferences' tab, see above). Extra folder shortcuts can be added or removed from the menu.

As for any important computer data, please backup variant files regularly.
When variants are stored in a shared file system, caution must be taken so that 2 people don't edit concurrently variants of the same gene.

Variant files use a simple XML representation format, suitable for processing by other applications. Furthermore, variants can be exported to tab-delimited flat text files that can be easily imported into spreadsheet applications.

Creating variants

Create variants either from the 'Variants' menu, or from a nucleotide selection in the transcript track and its associated context menu (by right-clicking inside the selection).

Once you have specified variant basic properties (position and type of change), the annotation window pops up:

Application of HGVS recommendations

The HGVS recommendations for the description of sequence variants implies that for all descriptions the most 3' position possible is arbitrarily assigned to have been changed. Application of this recommendation can make variant entering in Alamut® Visual sometimes disconcerting, since entering a variant may result in a variant located at a different position. The point is that both mutated sequences – entered and resulted – are identical.

For instance:

Variant entered	NM_000546.4(TP53):c.685_686del
Variant resulted	NM_000546.4(TP53):c.686_687del
Reference sequence	...CTCTGACTGTACCACC...
Mutated sequence – entered	...CTCTGAC--TACCACC...
Mutated sequence – resulted	...CTCTGACT--ACCACC...

Another case:

Variant entered	NM_000352.3(ABCC8):c.-52_-44del
Variant resulted	NM_000352.3(ABCC8):c.-41_-33del
Reference sequence	...GCAGGCGCGCGGAGCCAGCGGAGCCAGCTGAGC...
Mutated sequence – entered	...GCAGGCGC---------GCGGAGCCAGCTGAGC...
Mutated sequence – resulted	...GCAGGCGCGCGGAGCCAGC---------TGAGC...

Variant annotations

Classification

Variants can be classified using two classification schemes:

• A 3-classes scheme:
  • Not pathogenic
  • Unknown pathogenicity
  • Pathogenic
• A 5-classes scheme:
  • Class 1 - Certainly not pathogenic
  • Class 2 - Unlikely pathogenic
  • Class 3 - Unknown pathogenicity
  • Class 4 - Likely pathogenic
  • Class 5 - Certainly pathogenic

You can choose the classification scheme of each variant in the variant annotation window:

The default classification scheme can be set in the Options dialog box (menu 'Tools' > 'Options' > 'Preferences' tab) and pathogenicity classes and colors can be customized as well:

Occurrences

Beside the pathogenic status of the variant, you can record different occurrences of the same variant. To create an occurrence, click on the 'New Occurrence' button. In the occurrence panel, you can then enter specific information about the case at hand. Fields RNA Analysis, Phenotype and Comment are enabled with a rich text editor.

Edit Comment

Once you have created (or modified) an occurrence, the annotation window gets updated. At this point, you should save your changes:

• To modify an existing occurrence, double-click in the occurrence list.
• To remove an occurrence, select it (left click in the occurrence list) and click 'Delete Occurrence'.
• To delete the variant entirely, click the 'Delete' button at the bottom of the window.

Graphical display of variants

Variants are displayed graphically in the main Alamut® Visual window, in the transcript track, above the sequence:

Substitutions, deletions and indels are represented as rectangles, and insertions and duplications as discs at the point of insertion. The color of variant graphic items depends on pathogenicity annotations. By default:

3-classes scheme	5-classes scheme
Not pathogenic:  green	Class 1- Certainly not pathogenic  green
	Class 2 - Unlikely pathogenic  light green
Unknown pathogenicity:  yellow	Class 3 - Unknown pathogenicity  yellow
	Class 4 - Likely pathogenic  orange
Pathogenic:  red	Class 5 - Certainly pathogenic  red

To re-open a variant annotation window, click on its graphical representation.

© 2020 Interactive Biosoftware - Last modified: 30 December 2017