Somatic Variants

Please note: in order to use Cohort Browser on the Platform, an Apollo License is needed.

The results here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga."

Using Somatic Variants in Cohort Browser

• You can only have one type of variant per view in the cohort browser. As an example, you can only have somatic variants or the genomics tab available, but not both at the same time.

• Somatic variant data must be part of the data ingestion process to show the Somatic Variants Tab

• IF somatic data is present, this is the view you will see (with the somatic variant tab highlighted in dark blue)

  

Features of the Somatic Variants Tab

Overview

Here is your view when selecting the Somatic Variants Tab.

There are 3 sections: Variant Frequency Matrix, Lollipop Plot, and Variants Table

Variant Frequency Matrix (Oncoplot)

• Gene sorting (rows of the plot): gene names in descending order of percent of affected samples

• Sample sorting (columns of the plot): samples having the greatest number of mutated genes across all genes, independent of top mutated genes, in descending order

• Color coded by consequence (this is indicating counting consequences deemed 'HIGH' or 'MODERATE' impact, using Ensembl VEP v109)

• These features will also work while comparing cohorts.

• You can also hover over the patients tiles individually for more information.

Lollipop Plot

• One gene / canonical protein at a time

• Each lollipop will be color coded by consequence

• Search Bar: The user is able to navigate to a canonical protein by entering a gene symbol

• Interaction between Lollipop chart and the Somatic Variants Table

• The user can select (click) a single amino acid change (one lollipop) to quickly filter the somatic variants table

• These features will also work while comparing cohorts.

• You can also hover over the patients tiles individually for more information.

  

Variant Data Table

This is a tabular version of the data that you see. You can quickly filter this data while using the lollipop plot (described above) or by filtering on any of the column headers in the table.

Resources

Full Documentation

Cohort Browser Documentation

Chart Types

To create a support ticket if there are technical issues:

1. Go to the Help header (same section where Projects and Tools are) inside the platform

2. Select "Contact Support"

3. Fill in the Subject and Message to submit a support ticket.