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 collectionsby 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.

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. To create a new Gene Set, click on the Actions button (Figure 11.1) in the Genes menu and select Create Gene Set.

Figure 11.1. Create a gene set from Settings & More > Genes

From here, you can give your gene set a name and description and then paste in the desired genes. Click Create to create the set

11.2. View available Gene Sets

The Genes page has two tabs at the top of the page: 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 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 list of available gene sets to add the genes to

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. If you select a set, this will populate the filter with all of the genes in the set as shown in Figure 11.2.

Figure 11.2. Filter variants based on presence in a gene in a gene set

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