Targeted Gene Panel Analysis Software

Targeted gene panel sequencing is a form of next-generation sequencing that focuses sequencing reads on a defined set of clinically relevant genes rather than the entire exome or genome. Panels range from small focused tests covering a handful of genes, such as a BRCA1/2 panel, to comprehensive genomic profiling panels covering several hundred genes. The advantage over exome and genome sequencing is depth: by concentrating reads on target regions, panels routinely achieve 300x or greater mean coverage, enabling confident variant calling at low allele frequencies and reducing the number of incidental findings. Panels also produce smaller data files, faster analysis times, and simpler analytical validation, making them the most operationally efficient entry point for clinical NGS programs.

A typical targeted gene panel produces over 2,000 raw variant calls per sample. The role of tertiary analysis software is to systematically reduce that list to a short set of clinically significant candidates through a configurable filter chain. A standard germline panel workflow applies sequential filters (zygosity, genotype quality, internal cohort frequency via VSWarehouse, and ClinVar classification), reducing thousands of variants to single-digit actionable findings ready for ACMG interpretation. The exact filter configuration depends on the panel design, clinical indication, and laboratory validation. VarSeq's filter chains are saveable and reusable across samples, ensuring consistency and reducing per-case hands-on time.

A targeted gene panel sequences only the genes included in the panel design, while whole exome sequencing (WES) sequences all protein-coding regions of the genome, approximately 20,000 genes. Panels deliver deeper, more uniform coverage of their target regions at lower cost and faster turnaround than exome sequencing, and produce fewer variants to review. WES is broader and better suited for cases where the underlying gene is unknown, such as undiagnosed rare disease, while panels are appropriate when the clinical indication maps to a defined gene set. For a detailed comparison of assay types and when to use each, see WES vs WGS.

Yes. CNV detection from panel sequencing data is supported in VarSeq via the VS-CNV algorithm. Multi-exon deletions and duplications are clinically significant in several hereditary cancer genes (BRCA1, APC, MLH1) and other disease genes, but are missed by standard SNV/indel callers. VarSeq detects these events directly from panel read depth data, within the same analysis session as small variant calling, eliminating the need for a separate MLPA assay in most cases. Detection sensitivity depends on panel design and coverage uniformity; labs configure CNV detection thresholds as part of their analytical validation.

VarSeq supports any targeted NGS panel that produces a VCF file, regardless of the sequencing platform or secondary analysis pipeline used. This includes hereditary disease panels (hereditary cancer, cardiac, neurological, metabolic), comprehensive oncology profiling panels (TruSight Oncology 500 and others), carrier screening and prenatal panels, and pharmacogenomics panels. Each panel type has dedicated filter chain configurations, classification frameworks (ACMG for germline, AMP for somatic), and report templates. Labs can configure and save panel-specific workflows that are reusable across samples and locked for validation purposes.

VarSeq is designed for use in CAP/CLIA-accredited clinical laboratories. The platform produces deterministic results: the same input produces the same output every run, a prerequisite for reproducibility documentation under CLIA. Every analysis records the exact software version, annotation database versions, and filter configuration used, providing the audit trail CAP inspectors require to reproduce and justify any historical result. BED file region filtering restricts analysis to validated panel regions, coverage QC flags sub-optimal regions and must-call hotspot sites, and versioned pipeline locking prevents unvalidated configuration changes from affecting production results. Golden Helix operates under an ISO 13485-certified quality management system, and VarSeq Dx is CE marked under IVDR 2017/746.