Table 3.

Available diagnostic assays for detecting NTRK fusions.

Assay Type	Advantages	Limitations	Turnaround Time	Main Role in Potential Diagnostic Algorithms
IHC	Commonly available Limited cost Minimal tissue required Allows correlation with histology Confirms protein expression panTRK antibody available	Low sensitivity or specificity in specific settings No information about the fusion partner	1–2 days	Screening
FISH	Minimal tissue required High sensitivity and specificity although false negative results are possible	Specific lab facilities required and expertise for interpretation No information about the fusion partner One probe-one gene evaluation, thus time-consuming and higher costs	3–5 days	Confirmatory
RT-PCR	Limited cost High sensitivity and specificity	Requires knowledge about the fusion partners before testing and specific primers must be prepared Good pre-analytics required to preserve RNA	5–7 days	Confirmatory
Real time-PCR	Limited cost High sensitivity High specificity	Good pre-analytics required to preserve RNA It does not provide information regarding the specific fusion partners and it evaluates a pre-determined set of rearrangements, thus novel or rare fusions will be missed	5–7 days	Screening/Confirmatory*
RNA-NGS	Evaluation of all potential fusions in a sample if Total RNA is analyzed Provides characterization of fusion partners High sensitivity High specificity	Specific lab facilities required and expertise for interpretation High costs Good pre-analytics required to preserve RNA Longer TAT	1–3 weeks	Screening/Confirmatory*
DNA-NGS	It can provide an overall characterization of tumor molecular profile (mutations, CNV, tumor mutation burden…) Provides characterization of fusion partners High sensitivity with some caveats High specificity	Chance of detecting non-significant chromosomal rearrangements Potential low sensitivity for specific fusions Specific lab facilities required and expertise for interpretation High costs Longer TAT	1–3 weeks	Screening/Confirmatory*
DNA/RNA-NGS	It provides the most complete characterization of tumor molecular profile (mutations, CNV, tumor mutation burden, fusions…) Provides characterization of fusion partners High sensitivity High specificity	Specific lab facilities required and expertise for interpretation High costs Longer TAT	1–3 weeks	Screening/Confirmatory*

* depending on each laboratory diagnostic routine workup of a sample (for instance based on tumor type) and available resources/facilities.