Relying solely on Next-Generation Sequencing (NGS) is insufficient for HER2 testing in biliary tract cancers. Data shows NGS misses up to 15% of patients with HER2 overexpression detected by immunohistochemistry (IHC). Performing both tests is essential to avoid denying patients effective targeted therapies.

Despite identifying resistance mutations, evidence is insufficient to definitively link a specific alteration to a subsequent drug's efficacy. Biomarkers provide crucial context for clinicians, but do not yet dictate a precise treatment path, highlighting the need for clinical judgment.

For extrahepatic cholangiocarcinoma, obtaining a sufficient tissue sample for diagnosis and molecular profiling can be extremely difficult. Circulating tumor DNA (ctDNA) testing, or liquid biopsy, serves as a crucial alternative in these cases, providing a non-invasive method to secure a diagnosis and identify actionable mutations when a traditional tissue biopsy is not feasible.

When a biliary tract tumor has both an FGFR2 fusion and HER2 positivity, oncologists may prioritize targeting the FGFR2 fusion. They reason that fusions are often early, clonal, and homogenous driver events, making them a more reliable therapeutic target than HER2, which can be expressed heterogeneously.

DNA-based NGS can fail to detect clinically actionable fusions in NSCLC due to assay design limitations (low sensitivity). It can also report fusions of unclear significance (low specificity). Integrating RNA-based NGS is critical to reliably identify true driver fusions and clarify ambiguous DNA findings.

The technology and breadth of molecular testing panels for GIST are rapidly evolving. A patient whose tumor tested negative for driver mutations in the past should be considered for re-testing with current, broader panels. This may uncover previously undetectable alterations like FGFR translocations and open up new treatment options.

Early studies found FGFR2 fusions in ~15% of patients, skewed by testing heavily pre-treated individuals. As testing moves to the first-line setting, the true prevalence appears to be much lower (5-8%), which has major implications for clinical trial design and prevalence estimates.

Standard DNA-based Next-Generation Sequencing (NGS) can miss critical gene fusions, like ROS1. RNA sequencing is much more effective at identifying these specific alterations, so clinicians should ensure their chosen assay includes RNA analysis to avoid missing opportunities for targeted therapy.

For critical driver mutations like ROS1 and ALK fusions, relying solely on DNA-based Next-Generation Sequencing (NGS) is insufficient. A study showed that a significant portion of these fusions are only detectable via RNA sequencing. Clinicians must verify that RNA analysis was included in NGS reports to avoid missing effective targeted therapies for one in five potential patients.