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Using Saved Gene Sets for Analysis

This tutorial shows how to view all variants present in a proband for a set of genes previously saved in Mosaic. This tutorial uses the gene set created in the Creating Gene Sets from HPO Terms tutorial.

We will walk through the steps taken in the above video, describing how Mosaic lets us share analyses with everyone with access to the Mosaic project.

  1. We start by selecting the proband sample from the Samples page
  2. We can then launch any applications by clicking on the Launch App button
  3. There are a few options, but since we had selected a sample at launch, this is entered by default. The sample is part of a pedigree, so by default, gene.iobio will launch for the whole family. Finally, we can manually enter genes to analyse, or choose to use any saved gene or variant sets. We will choose the gene set created in a previous tutorial here - called Test Gene Set
  4. When we hit Launch, gene.iobio launches and annotates all variants in the 19 genes contained in the gene set
  5. If any variants of interest (e.g. rare de novo variants, or pathogeic ClinVar variants), these will be highlighted in the left menu. We can select the Genes to see all the genes that were analysed, or add additional genes in the menu bar
  6. Clicking the Add analysis button at the top right allows us to save this gene.iobio analysis back to Mosaic
  7. Saved analyses can be found in the Analyses page in the left menu. When a new analysis is saved, it is listed as a Draft in the table. This means that it is only visible to you. To share the analysis with everyone else, select the analysis, then select Publish from the Actions. Selecting Launch from the Actions will reopen the gene.iobio exactly as it was saved

Related tutorials

  • Learn how to create gene sets from HPO terms here