Gene Panels

VarLens includes a gene panel system for region-based variant filtering. Create panels from gene lists, import from PanelApp, or generate interaction panels from StringDB — then apply them to filter variants by genomic coordinates.

Filter Sidebar

Select panels from the Gene Panels section in the filter drawer. Active panels restrict the variant table to genomic regions covered by the panel's genes (with configurable padding).

Control	Description
Add panel	Dropdown to select a panel for filtering
Padding	Base pairs added around each gene (0, 1kb, 5kb, 10kb)
Manage Panels	Opens the panel management dialog

Multiple panels can be active simultaneously — their regions are merged (union).

Panel Manager

Access via Settings > Gene Panels or Manage Panels in the filter drawer.

The manager shows all panels with name, version, source, gene count, and creation date. Actions per panel:

• Edit — modify name, version, description, or gene list
• Copy — duplicate the panel
• Export — save as BED file (choose assembly and padding)
• Delete — remove with confirmation

The footer shows the bundled gene reference database status (gene count, assemblies, build date).

Creating Panels

Click New Panel to open the editor. Enter a name, optional version, and description, then add genes.

Adding Genes

Autocomplete search — type a gene symbol in the search field. Results show the HGNC-approved symbol, full name, and locus group. Alias matches display the matched alias.

Paste a list — click Paste List to bulk-add genes separated by newlines, commas, or semicolons. All symbols are validated against the bundled HGNC gene reference.

Validation States

Status	Icon	Meaning
Approved	Green check	Current HGNC symbol, ready to save
Alias	Orange warning	Matched an alias or previous symbol — click Accept to resolve
Ambiguous	Orange warning	Alias maps to multiple genes — select the correct one
Unknown	Red X	No HGNC match — must be removed before saving

Panels can only be saved when all genes are in the Approved state (strict validation).

Importing from PanelApp

Click Import PanelApp to search and import expert-curated disease gene panels from Genomics England PanelApp (UK) or PanelApp Australia.

1. Enter a keyword (e.g., "kidney") or panel ID
2. Select region: UK, Australia, or Both
3. Choose a panel from the results
4. Set confidence level filter: Green only (diagnostic grade), Green + Amber, or All
5. Click Import

Imported panels track their source, version, and confidence threshold.

Generating from StringDB

Click StringDB Generate to create interaction panels from protein-protein interaction data.

1. Enter seed genes (paste or one per line)
2. Select a preset or configure custom parameters:
   • High-confidence physical — score >= 700, physical interactions only
   • Medium functional — score >= 400, functional network
   • Broad exploration — score >= 150, discovery mode
3. Click Generate

The resulting panel includes the seed genes plus their validated interaction partners.

How Filtering Works

When a panel is active, VarLens:

1. Looks up genomic coordinates for each gene in the panel using the bundled reference database
2. Applies the selected padding (e.g., +/- 5kb) around each gene
3. Merges overlapping intervals
4. Filters variants to only those within the resulting genomic regions

The coordinates are matched to the case's genome build (GRCh37 or GRCh38). Panel filtering works in both case view and cohort view.

Gene Reference Database

VarLens ships with a bundled gene reference database containing:

• ~45,000 HGNC genes with symbols, aliases, and metadata
• Genomic coordinates for GRCh37 and GRCh38 (from Ensembl)
• FTS5 full-text search indexes for fast autocomplete

The database is extensible to future assemblies (e.g., T2T-CHM13).