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Gene Panels

This page describes gene panels, how they are annotated and how they are used in scout.

General

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.

File format

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 ##

Example:

##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:

  1. choose "Save as..." in Excel and select "Comma Separated Values (.csv)" as the format
  2. 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.