The Biomarker Explorer page allows you to explore the presence of specific genes and variants across various cancer types. This interactive visualization helps you assess how well particular biomarkers are represented across datasets, supporting decisions around assay development, data analysis, or research focus.
To get starts, click the "Biomarker Explorer" card on the Marketplace page.
How to Use the Coverage Chart
The main chart displays a bubble matrix:
Y Axis = individual genes or variants
The default view displays the top 30 genes when comparing coverage across all cancers. Genes are displayed along the y-axis, organized alphabetically by official gene symbol.
X Axis = cancer types
Common cancer types are displayed along the x-axis. Each cancer type is annotated with the number of distinct patients diagnosed for this cancer. Cancer types are defined via OCM ICD10 code mappings.
Bubbles = Each bubble represents the amount of coverage for the intersected cancer type and gene.
Size of the bubble reflects the percentage or count (depending on your selected data representation).
By default, the values are presented as percents, ie. number of distinct patients / total distinct patients diagnosed, but coverage amount can also be represented as a count, ie. the number of distinct patients.
Hovering over a bubble shows exact values.
Filters and Controls
1. Search Genes
Find additional genes via the search bar, and click apply. Make sure to use the official gene symbols when searching for your gene of interest. Genes will be available to search if at least 12 patients have a variant on this gene.
2. Granularity
This toggle controls the y axis. It defaults to display genes, but can display variants after the user searches for specific genes.
Once genes have been searched and applied, toggle to variant view to explore individual variants. The variant view displays the number of distinct patients per reported mutation on the selected genes. Reported mutations are presented on the y-axis, labelled with the associated gene. Variants are visible in this view if at least 12 patients have coverage for it.
3. Coverage Threshold (%)
Note that bubbles with less than 12 patients will never be visible.
Set a minimum threshold to filter out low-coverage results.
Bubbles below this percentage will be filtered out from the chart.
4. Data Representation
Percentage: Shows the percentage of patients with coverage.
Count: Shows the raw number of patients with coverage.
5. Reset Button
Clears selected genes and resets the chart to its default state.
Interpreting the Chart
The biomarker coverage chart presents the number of distinct patients that have genomic alterations for common cancer types.
Larger bubbles = higher coverage.
Hovering over a bubble reveals the cancer type, gene, and exact value (e.g., “TRP53 – Gastro/Esophageal Cancer – 34.3%”).
If your gene is not available to search, click to submit your interest in this gene.
Clicking on a Bubble to create a Cohort
To quickly build out a cohort using a desired gene/cancer type combination, click on a bubble.
