Molecular testing is now central to cancer care. Targeted therapies, immunotherapy biomarkers, and clinical trial eligibility all hinge on the accuracy and breadth of a tumor’s molecular profile.
Clinicians today are faced with an increasingly complex question: Should I order a single gene test, a hotspot panel, or comprehensive genomic profiling (CGP)? The answer depends on clinical context, but the trend is clear: broad-based testing is often the most efficient and clinically actionable strategy.
CGP uses next-generation sequencing (NGS) to assess hundreds of cancer-related genes in parallel. Modern panels detect a wide range of alterations, including:
- Single-nucleotide variants (SNVs)
- Insertions/deletions (indels)
- Copy number alterations (CNAs)
- Gene fusions and rearrangements
- Tumor mutational burden (TMB) and microsatellite instability (MSI)
Advantages:
- Tissue efficiency: One test, minimal input
- Therapeutic breadth: Captures rare and uncommon alterations
- Future-proofing: Enables clinical trial matching and anticipates resistance mechanisms
- Improved turnaround: Many CGP assays now return results in <10–14 days
In cancers such as non-small cell lung, prostate, cholangiocarcinoma, and many rare or advanced-stage malignancies, broad testing up front can directly impact therapeutic decision-making and spare the patient repeated biopsies or delays.
When Targeted Panels May Be Appropriate
While CGP is increasingly adopted as a first-line test, there are select cases where single-gene or hotspot testing remains appropriate:
Single Gene Testing
- When a specific alteration is strongly suspected based on histology or clinical features (e.g., EGFR in young, non-smoking NSCLC patients)
- Where rapid turnaround is essential, and results will drive an immediate treatment decision
- When tissue or financial constraints preclude broader testing
Hotspot Panels
- In tumors with a well-defined mutational landscape, such as colorectal cancer (KRAS, NRAS, BRAF) or melanoma (BRAF V600)
- As a reflex approach aligned with guideline-directed companion diagnostics
However, it’s essential to acknowledge the limitations: these panels frequently overlook fusions, CNVs, or non-hotspot mutations that may have therapeutic implications. They are also not designed to capture biomarkers like TMB or MSI that may inform immunotherapy eligibility.
Studies consistently show that a significant proportion of patients with advanced cancers harbor actionable alterations that are only detected through broader genomic profiling. For example,
- MET exon 14 skipping, RET, NTRK, or ALK fusions in NSCLC may be missed by DNA-only hotspot panels
- TMB-high or MSI-H status may go undetected, excluding patients from immune checkpoint therapy
- Emerging targets, such as FGFR2 fusions in cholangiocarcinoma or NTRK fusions across tumor types, require broader assays to be identified
Comparative Analysis
| Factor | CGP | Hotspot Panel | Single Gene |
| Alteration types covered | SNVs, InDels, CNVs, fusions, TMB, MSI in multiple genes | Limited SNVs/indels in a limited set of genes | Mutations detected in one gene only |
| Tissue efficiency | High | Moderate | High |
| Turnaround time | ~10–14 days | ~3–7 days | ~1–3 days |
| Therapeutic reach | Broad | Moderate | Narrow |
With increasing payer support and improved lab logistics, CGP is becoming the standard of care in many oncology settings, not just an option for refractory or rare tumors.
Unless contraindicated by tissue availability, urgency, or cost constraints, comprehensive genomic profiling should be considered as the first-line molecular test in patients with:
- Advanced or metastatic solid tumors
- Tumors with heterogeneous or poorly defined driver mutations
- Prior negative or inconclusive hotspot testing
- Interest in clinical trial enrollment or basket studies