Gene list
Add new case page > Case info screen > Select genes list
You can limit analysis to a gene list in the platform while creating a case. Select Custom Panel as your Case type. Choose between:
All genes. No limitation of the analysis.
Phenotype based genes (emedgene knowledge base). The list is automatically built from genes related to the HPO terms you entered for the case.
Existing gene list. Select one of the previously added gene lists from a dropdown list.
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).
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).
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.
Gene list modes
You can choose between two different modes of a gene list feature:
a) Gene panel mode (default): 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.
b) Boost genes mode (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.
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.
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.
You can alternatively 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 geneplease 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.
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