Which samples share a particular genomic alteration?

Objective

View all of the samples that share a particular genomic alteration of interest (e.g. TP53 mutation).

Skills Covered

  • Familiarity with the attribute drop down list
  • Familiarity with using the Short List of user selected/defined attributes.
  • Set Operation to create a new attribute derived from existing attributes.
  • Exporting a list of sample identifiers into a downloadable file.

Steps

  1. Get started with selecting samples on a TumorMap. The TumorMap UI provides users with a Select Attributes drop down that contains full list of sample annotations and attributes (long list) from which to choose attributes of interest, and a Short List that allows users more fine-tuned control of map operations.
  2. In this tutorial we will go through how to select attributes of interest, and then perform an intersection set operation to create a new custom attribute. Let’s say we are interested in viewing breast cancer samples that also have TP53 mutations, and then downloading a list of their sample IDs.
_images/caseShare-1.png
  1. In the Select Attributes drop down select Tissue and TP53_MUTATION attributes by typing in the beginning of the attribute name and clicking on the appropriate option in the list. This will copy the Tissue and TP53_MUTATION attributes from the long to the Short List
    NOTE: The tissue attribute might already be in the Short List as the default.
  2. In Select Attributes select BRCA Subtype by typing in the beginning of the attribute name and clicking on the appropriate selection in the list.
_images/caseShare-2.png
  1. Click on the Set Operation button. Its placement is shown in the graphic at the top of this page.
  2. In the popup window select Intersection for the desired set operation and select TP53_MUTATION as the first attribute and Tissue as the second attribute. Next to TP53_MUTATION click on the value drop down and click on 1. Next to Tissue select the value BRCA; click on the Compute Set Operation button.
_images/caseShare-3.png
  1. Enter the desired name of this new custom group of samples (e.g. TP53_BRCA)
  2. Observe that the new group appears as a custom attribute in the Short List
  3. In the Short List, if TP53_BRCA does not have a primary-hot, click on the primary to select it for color display
  1. Observe that the TP53 BRCA mutants are highlighted in the map
_images/caseShare-4.png
  1. Go to the File menu, then Download and click on Node IDs
  2. In the popup window make sure that TP53_BRCA is selected
  3. Save this group to a local file using the browser’s file download functionality

NOTE: You can just copy the sample IDs to the local computer memory by clicking into the box that contains the IDs to highlight them and then right-click and select Copy