What Is Neurotrophic Tyrosine Receptor Kinase (NTRK) Fusion? Should Immunohistochemistry or NGS Be Performed?

Looking at the Tumor's Genes, Not Its Organ: NTRK Fusion and Choosing the Right Test

An NTRK fusion is a rare genetic change in which two genes are joined at the wrong place, and it can be treated with targeted drugs regardless of the organ in which the tumor arose. It occurs in fewer than one in a hundred common cancers; yet when it is found, TRK inhibitors markedly shrink the tumor in about 60 percent of patients. The challenge is catching this rare change with the right test: pan-TRK immunohistochemistry (IHC) is a fast and inexpensive screening method, whereas next-generation sequencing (NGS) shows the fusion directly. In this guide, we explain what an NTRK fusion is, in which tumors it is sought, the strengths and weaknesses of IHC and NGS, the testing algorithm recommended by ESMO and how treatment is planned if a fusion is found. We covered the basics of genetic testing in our article on next-generation sequencing (NGS) and the concept of tissue-agnostic treatment in our article on tissue-agnostic cancer treatments.

Why does this matter?

For many years, cancer treatment was planned according to the organ in which the tumor arose: one drug for lung cancer, another for colon cancer. NTRK fusion is one of the first examples that changed this approach. In 2018, larotrectinib became the first targeted drug approved solely on the basis of a genetic change, regardless of the tumor's organ. That is why knowing whether a patient carries an NTRK fusion can change treatment options across very different tumors, from lung to thyroid and from colon to sarcoma (the importance of genetic alterations on the ESCAT scale).

However, NTRK fusion is very rare in common cancers; thousands of patients must be tested to find a few. Moreover, not every test catches this fusion equally well: some methods miss a portion of fusions, while others can give a positive result even without a fusion. That is why patients and physicians who see "pan-TRK positive" on a pathology report or "no NTRK fusion detected" on a genetic report need to know what the result does and does not show. For other biomarkers on pathology reports, see our articles on the PD-L1 test and HER2 concepts.

What is NTRK fusion?

An NTRK fusion occurs when the NTRK1, NTRK2 or NTRK3 gene, which encodes the TRK receptors, breaks and joins another gene. The resulting fusion protein stays permanently switched on without waiting for a signal and sends the cell a constant signal to divide. It is rare, but when found, it can be treated with targeted drugs called TRK inhibitors.

What do TRK receptors normally do?

TRK receptors (TRKA, TRKB and TRKC) are found mainly in the nervous system. They switch on briefly when signaling molecules such as nerve growth factor bind to them; they contribute to the development and survival of nerve cells, to the perception of pain and balance, and to the regulation of appetite and body weight. The characteristic side effects of TRK inhibitors, such as dizziness, weight gain and pain that appears when the drug is stopped, also stem from these normal functions.

In a fusion, the kinase portion of the NTRK gene (the "motor" that transmits the signal) joins the front portion of another gene. The front portion of this fusion partner gene usually makes proteins pair up; as a result, the TRK kinase stays switched on spontaneously and permanently, without any outside signal. More than 80 different fusion partner genes that join NTRK genes have been identified to date; the best known are ETV6-NTRK3, TPM3-NTRK1 and LMNA-NTRK1. Because the fusion alone can drive tumor growth, drugs that block this signal often produce strong and durable responses.

In which tumors does NTRK fusion occur?

NTRK fusions occur in two very different groups. The first group comprises certain rare tumors: secretory breast carcinoma, mammary analogue secretory carcinoma of the salivary gland, infantile fibrosarcoma of early childhood and cellular congenital mesoblastic nephroma (a type of kidney tumor in infants). More than 90% of these tumors carry a fusion; indeed, the fusion helps establish the diagnosis itself. The second group includes common cancers such as lung, colon, breast, thyroid and head and neck cancer, melanoma, sarcomas and brain tumors; in these, the fusion is mostly found in less than 1% (types of carcinoma).

Among common cancers, subgroups in which NTRK fusion is somewhat more frequent have also been described. In colon cancer, fusions are concentrated particularly in tumors with high microsatellite instability (MSI-H) and normal RAS and BRAF genes (colon cancer, the MSI-H concept). In thyroid cancer, they have been reported more often, especially in younger patients and those exposed to radiation. In lung cancer, they are sought in tumors lacking other driver alterations such as EGFR, ALK, ROS1 or KRAS (lung cancer). The fusion rate is also higher in pediatric tumors and high-grade brain tumors than in adult carcinomas (brain tumors).

Which tests are used to look for NTRK fusion?

There are four main ways to demonstrate an NTRK fusion, and each looks at a different level. Pan-TRK immunohistochemistry shows the TRK protein with a brown stain on a tissue section. FISH (fluorescence in situ hybridization) looks under the microscope for a break in a single NTRK gene. DNA-based NGS reads hundreds of genes at once. RNA-based NGS, in turn, reads the messenger RNA transcribed from genes and shows the fusion junction directly (guide to RNA sequencing). All of these tests can be performed on tumor tissue obtained by biopsy or surgery and stored in paraffin blocks.

Pan-TRK immunohistochemistry: strengths and weaknesses

The antibody used in pan-TRK IHC recognizes the kinase region shared by all three TRK proteins. Because very little TRK protein is normally present in adult tissues, distinct brown staining in tumor cells suggests a fusion protein. Where in the cell the staining appears can also offer a clue: staining may be seen in the nucleus with ETV6-NTRK3 fusions, in the cytoplasm with some NTRK1 fusions and at the nuclear membrane with the LMNA-NTRK1 fusion.

The largest validation study of IHC to date came from Memorial Sloan Kettering Cancer Center in the United States. Among the 33,997 patients examined in this study, an NTRK fusion was found in 87 (about 2.6 per 1,000). With RNA-based NGS as the reference, the overall sensitivity of pan-TRK IHC was 87.9% and its specificity was 81.1%. In other words, IHC caught about 88 of every 100 fusion-positive tumors, while giving a false-positive result in about 19 of every 100 tumors without a fusion.

Behind these overall figures lie two important details. First, while IHC almost always caught NTRK1 and NTRK2 fusions, it missed about one in five NTRK3 fusions (sensitivity 79%). The ETV6-NTRK3 fusion in infantile fibrosarcoma and secretory carcinomas falls squarely in this group; therefore, a negative IHC does not exclude a fusion in these tumors. Second, in tumors with neural or smooth muscle features (such as some sarcomas and brain tumors), normal TRK protein can stain even without a fusion; in these tumors, IHC is not a reliable screening method.

DNA or RNA? Why can't NGS catch every fusion?

Our genes consist of segments called exons, which carry the recipe for the protein, and the intervening regions between them called introns. In fusions, the break usually occurs within introns. In the NTRK2 and NTRK3 genes, some introns are tens of thousands of letters long; for economic reasons, most DNA-based panels do not read the whole of these long introns. If the break falls in an unread region, the fusion does not appear on the DNA test. In the same MSK study, the sensitivity of DNA-based NGS compared with the RNA test was 81.1%; that is, about one in five fusions was missed by the DNA panel.

With RNA-based NGS, the situation is different: when the cell produces messenger RNA, it already removes the introns. As a result, the junction between the fusion partner gene and the NTRK gene sits side by side in the fusion RNA and is read directly. The RNA test also shows that the fusion is actually "working," meaning that RNA destined to be translated into protein is being produced. Its weakness is that RNA is much more fragile than DNA; the test may fail in samples that are old, have been left in formalin for a long time or contain very few tumor cells.

Liquid biopsy (ctDNA) tests, which look at tumor DNA circulating in the blood, can also look for NTRK fusions; however, because they are DNA-based and the amount of tumor DNA in the blood can be low, they are more likely to miss fusions. Finding a fusion on a liquid biopsy is meaningful; not finding one does not exclude a fusion and should, where possible, be followed by tissue testing.

Immunohistochemistry or NGS: which should be done?

The short answer: for a treatment decision, the fusion must be demonstrated by NGS, preferably with a panel that includes RNA; IHC is a screening tool along the way, not a decision tool. ESMO's 2019 recommendations base the choice on tumor type. In rare tumors where the fusion is very common, the goal is confirmation, and FISH, RT-PCR or targeted RNA panels are sufficient. In common cancers where the fusion is rare, the goal is screening; the best option is a broad NGS panel that reliably detects NTRK fusions, and RNA-based sequencing is preferred if RNA quality allows.

The place of pan-TRK IHC in this algorithm is as a pre-screen when NGS cannot be done promptly, tissue is scarce or cost is decisive: if IHC is negative and the tumor has no neural or smooth muscle features, a fusion is unlikely; if IHC is positive, the result must be confirmed by NGS. Today, because many alterations such as EGFR, ALK, KRAS, BRAF, HER2, MSI and TMB need to be assessed together in many advanced cancers, a broad NGS panel that includes NTRK is often the route that makes the best use of both tissue and time.

Who should be tested for NTRK fusion?

Because the drugs approved for NTRK fusion are currently used in solid tumors that are advanced (metastatic) or whose surgical removal would cause serious problems, testing is mainly recommended for these patients. Since it is impossible to know in advance in which tumor a fusion will turn up, it is recommended that NTRK be tested as part of a genetic panel in patients with advanced solid tumors. In some situations, however, the likelihood of a fusion is clearly higher and testing becomes a priority (what is metastasis?).

If a fusion is found: TRK inhibitors

The drugs used in patients with a confirmed NTRK fusion are oral targeted drugs that switch off the fusion protein by fitting into the signaling pocket of the TRK kinase (how to take oral targeted pills). All three are FDA-approved regardless of the tumor's organ. The approvals are based on single-arm "basket" trials; that is, patients with different tumor types were enrolled in the same trial, and no comparison group was used. Because the fusion is so rare, a randomized trial is almost impossible to conduct.

Larotrectinib (Vitrakvi) is the first drug to target TRK alone. It received accelerated approval in November 2018 and full approval in April 2025. In the 339-patient analysis underlying the full approval, the objective response rate was 60%, the complete response rate (the tumor disappearing on imaging) was 24% and the median duration of response was 43.3 months. In a 93-patient analysis in children, the response rate reached 84%; the 3-year overall survival rate was 93%. Because it is available as capsules and as a liquid, it can also be used in infants.

Entrectinib (Rozlytrek) targets ROS1 and ALK in addition to TRK, and it crosses into the brain well. It was approved in August 2019. In an updated analysis of 121 adults, the response rate was 61.2%, the median duration of response was 20 months and the median progression-free survival was 13.8 months. In 11 patients with measurable brain metastases, the intracranial response rate was 63.6% (ALK-targeted treatments).

Repotrectinib (Augtyro) is a next-generation drug designed against resistance mutations. It received accelerated approval in June 2024. The response rate was 58% in 40 patients who had not previously received a TRK drug and 50% in 48 patients who had previously received a TRK drug and whose disease had progressed; in this second group, the median duration of response was 9.9 months. It is therefore an important option, particularly for patients whose disease progresses after first-generation drugs.

The side effects of TRK inhibitors are mostly mild or moderate, but some are distinctive because they relate to TRK's normal functions in the nervous system: dizziness and balance problems, weight gain, altered taste, numbness and tingling, muscle aches, constipation and elevated liver enzymes. Bone fractures have also been reported with larotrectinib. Because some patients may experience temporary pain when the drug is stopped, treatment should not be discontinued without consulting the physician.

What happens if resistance develops?

Responses to TRK inhibitors often last a long time, but resistance can develop over time. The most common cause of resistance is new mutations that alter the pocket in which the drug sits: the NTRK1 G595R or NTRK3 G623R mutations in the "solvent front" region, and mutations in the "gatekeeper" and xDFG regions. Repotrectinib and other next-generation drugs in development may be effective against a substantial share of these mutations. Less often, the tumor bypasses TRK and begins using another signaling pathway, such as KRAS, BRAF or MET; in this "off-target" resistance, a new TRK drug alone may not be sufficient (how do cancer cells become resistant to treatment?).

The situation in Türkiye

Questions to ask your doctor

• Has my tumor been tested for NTRK fusion? If so, by which method (IHC, DNA-NGS, RNA-NGS)?
• Does the NGS panel used include RNA, or does it cover the NTRK introns?
• If my pan-TRK result is positive, has it been confirmed by NGS? If it is negative, does this result completely exclude a fusion?
• Is there enough tissue for testing, or is a new biopsy needed? Is a liquid biopsy an option?
• If a fusion is found, how can I access a TRK inhibitor? Could I take part in a clinical trial?
• If the disease progresses during treatment, will the cause of resistance be investigated again?

Frequently Asked Questions

What is NTRK fusion?

An NTRK fusion occurs when the NTRK1, NTRK2 or NTRK3 gene breaks and joins another gene. The resulting fusion protein stays permanently switched on and sends the cell a constant growth signal. It is found in about 3 in 1,000 of all solid tumors, but in more than 90% of certain rare tumors.

Should immunohistochemistry or NGS be used to test for NTRK fusion?

For a treatment decision, the fusion must be demonstrated by NGS, preferably with a panel that includes RNA. Pan-TRK immunohistochemistry can be used for screening when access to NGS or tissue is limited; a positive result is confirmed by NGS, while a negative result does not fully exclude fusions, particularly NTRK3 fusions.

Which drugs are used if an NTRK fusion is found?

Larotrectinib, entrectinib and repotrectinib are TRK inhibitors with FDA approval regardless of the tumor's organ of origin. With larotrectinib, the objective response rate is 60% and the median duration of response is 43.3 months; repotrectinib is also effective in patients who developed resistance to a previous TRK drug.

Who should be tested for NTRK fusion?

In patients with advanced or metastatic solid tumors, testing for NTRK as part of a genetic panel is recommended. Secretory carcinomas, infantile fibrosarcoma, pediatric tumors, younger patients and tumors without another known driver alteration are priority groups.

Glossary

Gene fusion

The breaking and joining of two different genes to form a new, abnormal gene.

TRK receptor

A protein encoded by the NTRK genes that transmits signals such as nerve growth factor into the cell.

Kinase

An enzyme that can be switched on and off and transmits signals by adding phosphate to other proteins.

Pan-TRK immunohistochemistry

Staining of a tissue section with an antibody that recognizes all three TRK proteins at once.

NGS (next-generation sequencing)

A genetic testing method that reads many genes at the same time.

Exon and intron

The segments of a gene that carry the protein recipe (exons) and the intervening regions between them (introns).

FISH

A test that uses fluorescently labeled probes to show a break or rearrangement in a gene under the microscope.

Sensitivity and specificity

The proportion of people with a condition whom a test correctly detects (sensitivity) and of people without it whom the test correctly finds negative (specificity).

Tissue-agnostic approval

Approval of a drug based on the genetic alteration a tumor carries rather than the organ in which it arose (also called tumor-agnostic approval).

Solvent front mutation

A type of mutation that prevents the drug from fitting into the kinase pocket and causes resistance to TRK inhibitors.