This page describes gene panels, how they are annotated and how they are used in scout.
Scout is developed to be used in a clinical setting and therefore gene panels is a central concept. The gene panels describes a set of genes with additional information that is often associated with a disease or a disease group. A case can then be associated with one or several gene panels.
The gene panel is a tab separated text file with a header that describes the columns and one line for each gene entry.
The columns that will be used by scout is the following:
- hgnc_id(int) This identifies the gene. Mandatory
- hgnc_symbol(str) This is used for sanity check when humans look at the file. Optional
- disease_associated_transcripts(str) ','-separated list of manually curated transcripts. Optional
- genetic_disease_models(str) ','-separated list of manually curated inheritance patterns that are followed for a gene. Optional
- mosaicism(str) If a gene is known to be associated with mosaicism this is annotated. Optional
- reduced_penetrance(str) If a gene is known to have reduced penetrance this is annotated. Optional
- database_entry_version(str) The database entry version is a way to track when a a gene was added or modified. Optional
Each gene in a gene panel have to be identified with a hgnc id
File format 2
There is also an option to include all information about a panel in the header of the file. This could make uploading easier, just a matter of taste. In this case include a header with metadata, each of these lines are key-value separated by
=. The meta data lines should start with
##panel_id=panel1 ##institute=cust000 ##version=1.0 ##date=2016-12-09 ##display_name=Test panel #hgnc_id hgnc_symbol 7481 MT-TF ... ... ...
Notes on entries
- hgnc_id: This one have to be a valid hgnc id that exists in scout
- genetic_disease_models can be anyone in [AR,AD,XR,XD,MT,X,Y]
- mosaicism Any entry here will be interpreted as true
- reduced_penetrance Any entry here will be interpreted as true
- database_entry_version This should refer to a earlier version of the panel
Uploading a new gene panel version
You can upload a text file in Scout to update an existing gene panel. It should follow the format specified in this file: panel-example. The file is
; (semi-colon) separated, could also be tab separated.
You can also use this example Excel template as a starting point. When you are ready to update the gene panel simply:
- choose "Save as..." in Excel and select "Comma Separated Values (.csv)" as the format
- fill out the form in Scout and upload the "*.csv" file to update your gene panel
Upload from interface
Choose the menu in top left corner, click
Gene Panel. Then under 'new panel' the user can point to a csv file and fill in name and display name.
Upload with CLI
When uploading from CLI there are more options. Use
scout load panel --help for more information.