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Add a Gene List

Use the gene list manager to create gene lists and save them to your account or workgroup. You can create gene lists using any combination of the following methods:

• Import gene list (*.txt) files
• Merge existing gene lists
• Manually add genes
• Search for genes associated with specific phenotypes
• Search for genes associated with diseases listed in Genomics England PanelApp

Genes are added to a working list that you can review and refine before saving the final gene list.

1. Select the Settings icon or select Settings from the Account menu drop-down list.
2. Select the Gene Lists tab.
3. [Optional] Download a template to create a gene list as follows.
  1. Select Download Sample Gene List to download the template.
  2. In a text editor such as Notepad, follow input requirements to modify the gene list as needed.
  3. Save in *.txt file format.
4. Select Add Gene List.
5. Enter a name for the gene list.
6. To import genes from a gene list *.txt file, do as follows.
  1. Select the Add Genes tab.
  2. Select Import.
  3. Browse to the gene list (*.txt) file and select Open.
7. To add genes from existing gene lists in your account, do as follows.
  1. Select the Merge Gene List tab.
  2. Select a merge option.
    • Union—Adds all genes from the selected gene lists.
    • Intersect—Adds only the genes that are common to both gene lists.
  3. Select the checkboxes for up to five gene lists.
  4. Select Add.
8. To add genes manually, do as follows.
  1. Select the Add Genes tab.
  2. Enter one or more gene names separated by commas, spaces, or new lines. You can manually enter each gene or copy and paste a list from another source.
  3. Select Add.
9. To add genes associated with a specific phenotype, do as follows.
  1. Select the Search tab.
  2. Select Search by phenotype from the drop-down menu.
  3. Select a merge option.
    • Union—Adds all genes from the selected gene lists.
    • Intersect—Adds only the genes that are common to both gene lists.
  4. [Optional] Enter the maximum number of genes to return for each list.
  5. Select the Source drop-down arrow and then select one or more sources.
    • ILMN—Illumina proprietary database
    • Exomiser—Monarch Initiative Exomiser
    • GeL—Genomics England PanelApp
    • Phenopedia—Human Genome Epidemiology (HuGE)
    • HPO—Human Phenotype Ontology
  6. Enter a phenotype, and then select the appropriate phenotype from the search results list.
  7. Select Add.

    8. NOTE

    BaseSpace Variant Interpreter uses fuzzy matching when performing phenotype searches, and can return other potentially related genes.

10. To add genes associated with a specific disease name, do as follows.
  1. Select the Search tab.
  2. Select Search by disease name (panelApp) from the drop-down menu.
  3. Select a confidence level, High or All.
    • High—Diseases have strong evidence linking to the gene.
    • Intersect—Diseases have strong, medium, or low evidence linking to the gene.
  4. Enter a disease name, and then select the appropriate disease from the search results list.

    5. The search results list the disease name, PanelApp version, and number of associated genes.

  5. Select Add.
11. [Optional] Remove unwanted genes from the working list.
  1. Select a gene group or individual gene, and then select Delete.
  2. Select Clear List to remove all genes.
12. Select Save.
13. If a validation error occurs, remove the invalid genes from the list.
  1. To save the list with the invalid genes removed, select Delete All in the Invalid Gene Names dialog.
  2. To review and manually remove invalid genes, select Cancel in the Invalid Gene Names dialog, and then revise the list. The invalid genes are highlighted in red in the working list.