How to explore cohorts of genomic sequencing data in a customizable dashboard
Prior to working with a series report, ensure that you have set up your library and created a series. Learn more about setting up your library here. VCF files are required to work with the genomic sequencing series report.
Step 1. Create a Series Report
From the Library
Select the series you would like to work with and select "Create Series Report". This will open a dialog for you to provide a name, description and select the "BioBox WGS/WES" dashboard.
From the Workspace
Go to your workspace and select the "Series Report" tab. Create a new series report- provide a name, description, select a series and the BioBox WGS/WES Dashboard.
Step 2. Explore Data
Once you create your Series Report the widgets will begin to populate with observations computed from your data.
Mutational Rate Widget
This widget allows you to explore the mutation rate across all genes within your series. By default all mutational consequences identified in your series are selected. Using the drop down you can deselect specific consequences to narrow down your observations.
Within the table you can explore
- Gene Symbols
- Ensemble IDs
- # of mutations associated with each gene for the selected consequences
- The frequency of mutations for each gene + selected consequences across all of the experiments in your Series
- The number of samples with more than 1 mutation associated with the selected consequences per gene
Using " Add Filter" the genes can be further subsetted on the basis of mutational frequency, number of mutations and samples with more than 1 mutation. Once a desired gene list has been achieved, the gene list can be saved. This gene list can be used in the pathway enrichment widget.
Variant Frequency Widget
This widget allows you to identify the frequency of specific variants across your series and the specific records that were identified to have those variants.
Search for a variant using HGVS nomenclature and you will see the percentage and quantity of this variant across the experiments in your series.
The table will update to display the records associated with experiments where the variant of interest was identified. Selecting the menu icon in the top right hand corner of the table will allow you to customize the metadata properties that are displayed in the table. e.g. if you are interested in the impacts of Cell Type this metadata property can be selected and displayed in the table.
Filters can be applied to subset your cohort. Records can be filtered on the basis of any biological metadata that you track. This will reduce the number of experiments that are used in the calculation of variant frequency.
Let's say you have a Series of 334 experiments and want to see the frequency of variant [NC_000017.11:g.43124078G>C]. The variant frequency is 2.4% as 8/334 experiments within the series are identified to have the variant.
Now you want to see what the variant frequency is amongst glioma stem cell patients. Filtering on Cell Type is Glioma Stem cell will reduce the number of experiments identified with the variant.
The variant frequency is 1.6% as 6/334 experiments within the series are identified to have the variant.
The ClinVar Summary Widget enables you to see all ClinVar annotated variants for genes of interest.
Search for a gene and the table will display all of the ClinVar annotations and clinical metadata.
HGVS identifiers can be copied and used in the variant frequency widget.
The Pathway Enrichment Widget enables you to run an over representation analysis on gene lists that were saved from the Mutational Rate Widget.
Select a bar corresponding to a pathway to see all of the genes enriched in the contrast you have created + filters you have applied. Select a gene to obtain a description of the gene.
Use the mutation rate widget to identify genes that are high frequency mutants, save this gene list and explore the pathways and gene sets enriched across the high frequency mutants.
Search for a specific gene and explore observations across all datasets on the platform.
Type in a gene and select the type of observation you would like to see. Scroll through the plots to see your observations. Narrow down your results by searching for a specific record or file.
Any new data that is added to a genomic sequencing series will automatically be reflected in the Series Report.