Gene lists

VarSome Clinical offers 3 ways of creating a new gene list:

1. Copy and modify an existing gene list
2. Create a new gene list
3. Create a gene list from phenotypes

1. Copy and modify an existing gene list

The options to manage the existing gene lists are the following:

Gene lists can be copied by clicking on the "Copy" button .
Genes can be added or removed by clicking on the "Edit" button . Once you have finished editing the gene list, you can save the list with either the original name or with a new one.

2. Create a new gene list

• Click on "Create new gene list".
• A pop up form window appears, you just need to write a name for your gene list and paste the list of genes that you want to analyse. Important note: the gene names need to follow the HGNC (Hugo Gene Nomenclature Committee) standard (http://www.genenames.org/), if the gene names do not follow this rule you will get an error message after clicking on Save list.
  
  

3. Create a gene list from phenotypes

• Click on "Create gene list from phenotypes"
• Start by filling in a phenotype. By selecting All, phenotype matching records from HPO, MONDO and OMIM® will be available

• Click on phenotype from the drop down menu to add it to your phenotypes list. (You can right click any phenotype to remove it from the list)
• Select one or more phenotypes from your list to view the associated genes

• Finally select one or more genes to be added to your gene list

The methodology to generate a gene list from phenotype(s) has been changed. Previously, when making a gene list from phenotypes, we would include only those genes that are directly annotated with that phenotype. We have now extended this and instead first collect all diseases linked to the phenotype and then all genes linked to those diseases, as well as any genes directly linked to the phenotype. We already worked this way when adding phenotypes to analyses, so this change ensures we are consistent and also makes sure we don’t miss any genes when creating gene lists.

If you want to filter your gene list, you have to go to the Variant table page of the CNV analysis you performed and click on the filter icon on the left. Click on "Create" to create a new one and you will see a screen like the one below:

Click to add a Gene list filter for the specific phenotype you wish. Fill in the name of the filter set and save it in order to be applied on your analysis. 

Browsing through gene lists

• Search gene lists by name:

• Toggle custom view:
  
  
• Display gene lists sorted by name or update date: