Gene list

Add new case page > Case info screen > Select genes list

Select gene list

You can limit analysis to a gene list in the platform while creating a case. Choose between:

1. All genes

No limitation of the analysis.

2. Phenotype based genes

The list is automatically built from genes related to the HPO terms you entered for the case (per Emedgene knowledge base).

3. Existing gene list

Select one of the previously added gene lists from a dropdown list.

4. Create a new gene list

Generate a new virtual panel: add a List title and then add all the gene symbols one by one (Selection mode) or in a batch (Batch mode).

Note: Please use the up-to-date gene symbols approved by the Hugo Gene Nomenclature Committee. When adding gene symbols in a Batch mode, those genes that do not comply with HGNC standards will be automatically excluded from the gene list. These genes will appear for 3 seconds in a black error box at the bottom of the screen.

Selection mode

For each gene please follow the steps described below: Enter a gene symbol in the search box in the right panel (Candidate Genes) and select a matching symbol from a dropdown menu.

Batch mode

After selecting batch mode, paste a list of comma-separated gene symbols in the search box in the right panel (Candidate Genes).

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Gene list modes

You can choose between two different modes of a gene list feature:

1. Gene panel mode

The default option.

Analysis is limited to the selected gene panel, no variants in other genes are considered in the results. If this in silico panel is used for analysis of exome or genome data, the gene restriction may be lifted during manual analysis to "open-up" the entire exome or genome for analysis.

2. Boost genes mode

Enabled through checkbox.

Analysis is performed for variants in all the genes. Variants in the targeted genes get upgraded scores during prioritization by the AI Shortlist algorithm.

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How to filter variants by a gene list

1. Candidate Genes filter

To filter variants by the gene list, or remove the gene list restriction after the case has been delivered, go to the Analysis tools > Filters > Gene Filters > Candidate Genes filter.

2. Gene Lists filter created in a case

If you have run a case in All genes mode, you still can filter variants by a gene list. Go to Analysis tools > Presets > Gene Lists and select a list of interest. The Gene Lists filter presets can be defined by organization's manager.

3. Gene Lists filter created in Settings

Alternatively to creating a gene list filter in Presets, create and manage gene lists in Settings > Management > Gene lists.

First, fill in the List title and click Add button. Then add the gene symbols one by one (Selection mode) or in a batch (Batch mode).

• Selection mode - for each gene please follow the steps described below: Enter a gene symbol in the search box (Candidate Genes) and select a matching symbol from a dropdown menu.

• Batch mode: Paste a list of comma-separated gene symbols in the search box (Candidate Genes).

When you finished, press Save.

To view the Gene list in read-only mode, click on its name. By pressing the corresponding icons next to the Gene list's name, you can duplicate, edit or delete it. If a gene list has already been used by a case in the platform, you will only have the possibility to duplicate it.