CytoSure™ Interpret Software — Tips and Tricks

Monday 27 July 2015
Product types:

Gene Panel Scrolling

As an addition to the features supporting more streamlined analysis of targeted array designs such as the CytoSure Medical Research Exome Array, an interface allowing users to easily scroll through customisable “panels” of target regions has been created within CytoSure Interpret Software. The Gene Panel Scrolling plug-in is available via the Tools menu, and enables users to:

  1. Create multiple gene/targeted region panels.
  2. Select a specific panel.
  3. Assign a specific classification to all CNVs detected in the panel regions.
  4. Scroll through all genes in the panel to easily visualise the results in the panel regions.

In combination with the selective reporting of CNVs based on their classification (Tools -> Options… Classification -> Existing classifications -> Report?), the plug-in also provides a quick method for only reporting CNVs within the panel regions.

To use the plug-in:

1. Load a case and ensure that segmentation has been carried so that CNVs have been automatically detected.

2. Select Tools -> Gene Panel Scrolling to display the Region List Selection window.GPS13. If the panel has not yet been created, click the Create Region List button, enter a name for the panel in the Region List Name field and click Import annotations from file. The selected file should contain a list of gene names separated a line break. After clicking Open, the plug-in will search the annotation database for annotations matching the names in the file and create a region list using the associated co-ordinates. The new panel will then be available from the Region List drop-down box.

4. Select the appropriate panel from the Region List drop-down box.

5. Select the classification to be applied to all CNVs detected within the selected panel region using the Classification drop-down box.

6. Click Continue. This will result in the following:

  • The Initial Classification of all CNVs overlapping a region of the selected panel will be set to the selected classification.
  • A table displaying the regions contained in the selected panel will appear. Selecting a row of the table will result in the display of the associated panel region in the Genomic View.

GPS1To scroll through the CNVs located within the panel regions, use the CNV Regions table in the Genomic View and select those regions given the classification selected in step 5.

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CytoSure™ products are for research use only; not for use in diagnostic procedures.