11. Genes

Mosaic allows users to search variants based on genes or sets of genes, e.g. gene panels. Genes can be accessed both in projects or in collections by expanding Settings & More in the left menu, which will reveal the Genes option. Click on Genes to see a table of genes based on the reference genome associated with the project.

The Genes page is organized into tabs at the top — Table, Sets, and Charts. Table lists all available genes, Sets lists the gene sets you have defined, and Charts provides gene-level visualizations. The Launch App button can open a connected application for the selected genes, and the Actions button provides the gene-set and external-resource options described below.

11.1. Define a Gene Set or panel

A Gene Set is simply a list of genes, often called a panel when associated with clinical tests. Gene sets are stored for analysis purposes, for filtering variants, and for launching applications. To create a new Gene Set, click on the Actions button on the Table tab of the Genes page and select Create Gene Set.

In the Create Gene Set dialog, give your gene set a Gene Set Name and an optional Gene Set Description, then provide the genes in the Gene List field as a comma-separated list. You can copy and paste your own list of gene names; if you reached this dialog after selecting genes in the table, those genes are automatically populated in the field for you. Click Create to save the set.

11.2. View available Gene Sets

The Genes page has tabs at the top of the page including Table and Sets. Table shows a table of all available genes. Click on Sets to see all available sets and make any edits to them.

11.3. Edit Gene Sets

Genes can be added to and removed from Gene Sets from the Table tab. Just search for a gene, then select the check box next to the desired gene(s). From Actions, you can create a new gene set from the selected genes, or add or remove them from existing sets. To add to an existing set, for example, select Add to Gene Set and you will be given a list of available gene sets to add the genes to.

The same Actions menu also provides quick links to open the selected gene in external resources — for example View in MARRVEL and View in GTex — which is convenient when reviewing the function or expression of a candidate gene.

11.4. Filter variants based on Gene Sets

Once gene sets have been created, you can use them to extract variants from only these genes. To do this, select Variants from the left menu and view the table of variants. Click on Filters > Advanced Filters and then find the Genes filter. Click on this and you will have the option to specify individual genes or choose existing gene sets.

You can add additional genes, or remove genes from this list, combine it with other annotation filters, and then apply. The resulting list of variants will only include those that fall within any of the genes in the set - and that pass any already applied variant filters. See Variants for how gene and gene-set filters fit into the wider variant-filtering workflow.