Effective treatment of HER2-driven NSCLC requires more than just identifying mutations. HER2 is a multiplexed biomarker where both genetic mutations (TKD and non-TKD) and protein overexpression (via IHC) are independently actionable. Comprehensive testing is crucial to ensure patients are eligible for the full range of available targeted therapies, including TKIs and ADCs.

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.

When a colorectal tumor loses HER2 protein expression (IHC 0) but retains HER2 gene amplification via NGS, the decision to continue HER2-targeted therapy is guided by the amplification copy number. A low copy number argues against continuing the targeted regimen.

The specific type of HER2 mutation significantly impacts TKI efficacy. YVMA exon 20 insertions show the highest response rates. Other TKD (tyrosine kinase domain) mutations perform moderately well, while non-TKD mutations respond poorly. This molecular nuance is critical for predicting treatment success and managing patient expectations.

Oncologists distinguish between HER2 amplification (the target for ADCs like TDXD) and activating mutations. A patient whose tumor loses amplification but retains a mutation is considered "HER2 mutated," not "HER2 positive," and is generally not a candidate for ADC therapy.

For certain therapies like Enhertu, eligibility is based on immunohistochemistry (IHC), not NGS. Labs must run HER2 IHC in parallel because NGS, as a population-based test, can miss intratumoral heterogeneity (small clusters of positive cells) that IHC can detect, thus identifying more eligible patients for targeted therapy.

Clinicians ordering "NGS for lung" often misunderstand that Next-Generation Sequencing alone does not cover all actionable biomarkers, such as PD-L1 or HER2. This requires pathologists to interpret the clinician's intent and order a more comprehensive and appropriate test panel.

A negative liquid biopsy (ctDNA) result for HER2 amplification does not prove a patient is HER2-negative. The test's sensitivity is limited by tumor fraction in the blood. While a positive ctDNA result is highly specific and trustworthy, a negative result is simply 'not detected' and requires a tissue biopsy to definitively determine HER2 status for treatment decisions.

The standard HER2 tests were developed to identify HER2-positive tumors, not to precisely quantify low levels of expression. This creates a diagnostic challenge for identifying patients eligible for HER2-low targeted ADCs, requiring closer collaboration with pathology to interpret results that may be near the threshold, such as HER2-zero but with some minimal staining.