ALK Rearrangements in Lung Cancer

by Matthew Cecchini, MD PhD FRCPC
March 20, 2026

ALK (anaplastic lymphoma kinase) is a protein that plays a role in normal cell development. In healthy adult lung tissue, the ALK gene is essentially switched off. In approximately 3–7% of non-small cell lung cancers, a chromosomal rearrangement — a structural change in which a segment of DNA breaks and fuses to a different gene — causes ALK to be abnormally activated, producing a fusion protein that continuously drives cancer cell growth. The most common fusion partner is a gene called EML4, though many other partners have been identified. The result in every case is the same: a permanently switched-on ALK signalling pathway that the cancer cell depends on to survive. This dependency is the key to treatment, because drugs called ALK inhibitors can precisely target and block this abnormal protein, often achieving dramatic and durable responses. ALK rearrangements are now one of the most important targets in lung adenocarcinoma, and identifying them at diagnosis is essential to ensuring patients receive the most effective treatment available.

What the test looks for

In a normal cell, chromosomes remain intact, and genes stay in their correct positions. Occasionally, errors during cell division cause segments of chromosomes to break off and reattach to a different chromosome or to a different location on the same chromosome. When this happens to the ALK gene on chromosome 2, the result is an ALK rearrangement — also called an ALK fusion.

The most frequently seen rearrangement involves an inversion on chromosome 2 that fuses the EML4 gene to ALK, creating the EML4-ALK fusion gene. This fusion gene encodes an abnormal protein in which the signalling domain of ALK is permanently active. Over 20 EML4-ALK variants have been described, depending on the exact location of the break within EML4. Other fusion partners beyond EML4 — including KIF5B, TFG, KLC1, and others — are less common but equally important to identify because they all activate ALK signalling in the same way.

What matters clinically is not which specific fusion variant is present, but that an ALK rearrangement exists at all — because all ALK fusions predict sensitivity to ALK inhibitor drugs, regardless of the fusion partner.

Why is the test done

To determine eligibility for ALK inhibitor therapy. ALK inhibitors — including crizotinib (Xalkori), ceritinib (Zykadia), alectinib (Alecensa), brigatinib (Alunbrig), and lorlatinib (Lorbrena) — are highly effective in ALK-rearranged lung cancers and have essentially no meaningful activity in ALK-negative tumours. Identifying the rearrangement is the prerequisite for using these drugs.
To avoid less effective treatment. In patients with ALK rearrangements, ALK inhibitors are substantially superior to standard platinum-based chemotherapy in terms of response rate, duration of response, and quality of life. Testing ensures these patients are not undertreated with chemotherapy alone when a highly effective targeted option is available.
To guide the choice of an ALK inhibitor. Multiple generations of ALK inhibitors exist, with varying potency profiles, resistance patterns, and abilities to penetrate the central nervous system (brain and spinal cord). Knowing that an ALK rearrangement is present — and, in some settings, the specific fusion variant — guides the choice of drug to start with.
To monitor for resistance. When ALK-rearranged lung cancers progress on ALK inhibitor therapy, re-testing can identify the resistance mechanism and guide the choice of subsequent treatment.
To provide prognostic context. ALK-rearranged lung cancers, while aggressive in their untreated state, respond so well to targeted therapy that outcomes have improved dramatically. Patients with ALK-rearranged lung cancer often achieve prolonged disease control measured in years, not months.

Who should be tested

Current guidelines recommend ALK rearrangement testing for:

All patients with advanced or metastatic non-small cell lung cancer (NSCLC), regardless of histological subtype, smoking history, or clinical features, though ALK rearrangements are most common in lung adenocarcinoma.
Never-smokers or light smokers with NSCLC, in whom ALK rearrangements are more prevalent than in heavy smokers.
Younger patients with NSCLC, as ALK rearrangements tend to occur in a somewhat younger demographic than EGFR mutations or KRAS mutations.
Patients with resected early-stage lung adenocarcinoma, for whom some guidelines support ALK testing because of emerging data on adjuvant ALK inhibitor therapy.

In practice, ALK testing is performed as part of a comprehensive molecular panel at diagnosis for virtually all NSCLC patients at major cancer centres. It is rarely performed in isolation.

How the test is performed

ALK rearrangement testing can be performed using several different methods, each with distinct advantages and limitations. Most major cancer centres now use next-generation sequencing (NGS) as the primary platform, which simultaneously assesses ALK along with all other major lung cancer driver genes in a single test. Other methods may be used depending on the laboratory’s platform and the available tissue.

Immunohistochemistry (IHC)

Immunohistochemistry (IHC) uses a specific antibody (most commonly the D5F3 clone) to detect abnormal accumulation of the ALK protein in tumour cells. Because normal lung cells produce essentially no ALK protein, any strong positive staining is highly suspicious for an ALK rearrangement. IHC is fast, widely available, and inexpensive, and, with a highly sensitive antibody and a validated scoring system, it achieves excellent accuracy. It is used as a screening test in many settings. A positive IHC result is generally sufficient to initiate ALK inhibitor therapy without confirmatory testing, though some guidelines recommend confirmatory molecular testing for equivocal or weakly positive results.

Fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) was the original FDA-approved method for ALK testing and uses fluorescent probes that bind to either side of the ALK gene on chromosome 2. In a normal cell, the two probes sit close together. When a rearrangement has occurred, the probes separate — this “split signal” pattern indicates that a structural rearrangement has disrupted the ALK gene. FISH is highly specific but is labour-intensive and cannot identify the fusion partner. It is now used less commonly as a primary test where NGS is available, but may be employed to confirm equivocal IHC results.

Next-generation sequencing (NGS)

RNA-based NGS panels are particularly well suited to detecting ALK fusions because they directly sequence the messenger RNA produced by the fusion gene, allowing identification of both the fusion partner and the specific variant. DNA-based NGS panels can also detect ALK rearrangements, though RNA-based approaches are generally more sensitive for fusion detection. NGS provides the most comprehensive picture of a tumour’s molecular landscape and is the preferred approach when adequate tissue is available.

Liquid biopsy

Cell-free DNA testing from a blood sample (liquid biopsy) can detect ALK fusions, though sensitivity is lower than for point mutations such as those found in EGFR. This is because structural rearrangements are harder to detect in fragmented circulating DNA than single-nucleotide changes. Liquid biopsy is most useful for monitoring disease after a diagnosis has been established on tissue, or when tissue is insufficient for molecular testing. A negative liquid biopsy does not rule out an ALK rearrangement.

How results are reported

ALK results are reported as positive (rearrangement detected) or negative (no rearrangement detected), with a note on the testing method used. NGS reports will typically specify the fusion partner and variant where identified — for example, “EML4-ALK fusion, variant 1 (E13; A20)”. IHC reports will note the staining intensity and the scoring system used, with a positive result typically described as strong, diffuse cytoplasmic staining in the tumour cells.

Some NGS reports will flag a fusion of uncertain significance — a structural rearrangement involving ALK but with an uncharacterised partner or breakpoint. These results should be discussed with a thoracic oncologist, as the clinical significance may require further investigation.

What the result means

ALK rearrangement positive. An ALK fusion gene is present in the cancer cells. The tumour is driven at least in part by the abnormal ALK signalling pathway and is expected to respond to ALK inhibitor therapy. This is a highly actionable finding. For advanced disease, a next-generation ALK inhibitor — currently alectinib (Alecensa) or lorlatinib (Lorbrena) — is the recommended first-line treatment, based on clinical trials demonstrating superior progression-free survival compared to earlier-generation agents and excellent activity against brain metastases, which are common in ALK-rearranged lung cancer. Treatment with an ALK inhibitor is taken as a daily oral tablet, without the need for intravenous chemotherapy in the first-line setting.
ALK rearrangement negative. No ALK fusion was detected in the regions assessed by the test. ALK inhibitor therapy is not expected to be effective. The treatment plan will be guided by other molecular findings, PD-L1 expression, and the cancer’s stage. It is important to note that a negative result on one platform does not necessarily exclude an ALK rearrangement. If clinical suspicion remains high (for example, a young never-smoker with adenocarcinoma in whom all other driver mutations are absent), reflex testing with a different method may be considered.
Equivocal or borderline result. This can occur with IHC (weak or heterogeneous staining) or with FISH (a borderline percentage of rearranged cells). In these cases, an alternative or complementary testing method — most commonly RNA-based NGS — should be used to clarify the result before treatment decisions are made.

ALK inhibitors: generations and resistance

One of the most important aspects of ALK-rearranged lung cancer care is understanding that multiple generations of ALK inhibitors exist, and that the choice of drug — and the sequence of drugs over time — significantly affects long-term outcomes.

First-generation: crizotinib (Xalkori). The original ALK inhibitor, now rarely used as first-line therapy in ALK-rearranged NSCLC, because second- and third-generation agents have proven superior. Crizotinib also targets MET and ROS1, which are relevant in those specific settings.
Second-generation: ceritinib (Zykadia), alectinib (Alecensa), brigatinib (Alunbrig). More potent than crizotinib and more effective at penetrating the blood-brain barrier, which is critical because ALK-rearranged lung cancers have a high rate of brain metastases. Alectinib became a preferred first-line option based on the ALEX trial; brigatinib is also approved first-line based on the ALTA-1L trial.
Third-generation: lorlatinib (Lorbrena). The most potent ALK inhibitor currently available, with the broadest coverage of known ALK resistance mutations and the strongest central nervous system penetration. The CROWN trial demonstrated superior progression-free survival with lorlatinib over crizotinib, and it is now a preferred first-line option at many centres for patients with advanced ALK-rearranged NSCLC, particularly those with brain involvement or at high risk of brain metastases.

When a cancer progresses on an ALK inhibitor, the mechanism of resistance shapes the next treatment. Resistance can occur through mutations within the ALK gene itself (on-target resistance) or through activation of alternative signalling pathways that bypass ALK entirely (off-target resistance). Repeat molecular testing — often with both liquid biopsy and tissue biopsy — at the time of progression is important to guide the choice of subsequent therapy.

ALK rearrangements and brain metastases

Patients with ALK-rearranged lung cancer have a higher rate of brain metastases than patients with other NSCLC subtypes — both at diagnosis and over the course of treatment. This is one of the most important practical considerations in the management of ALK-rearranged lung cancer. Modern ALK inhibitors, particularly alectinib, brigatinib, and lorlatinib, are highly effective at controlling both systemic and intracranial disease because they penetrate the blood-brain barrier well. For patients who develop brain metastases during treatment with an ALK inhibitor, the decision between continuing ALK-directed therapy, switching to a later-generation agent, or adding radiation therapy is made on an individual basis. Brain MRI is often included in the staging and monitoring workup for patients with ALK-rearranged lung cancer.

ALK rearrangements: germline vs. somatic

Like EGFR mutations in lung cancer, ALK rearrangements are somatic — they arise within the cancer cells during the patient’s lifetime and are not inherited. Patients do not need to worry that their ALK rearrangement can be passed to their children, and family members do not require ALK screening on this basis.

What happens next

If an ALK rearrangement is found, your oncologist will recommend ALK inhibitor therapy. For advanced disease, alectinib or lorlatinib is currently preferred at most centres. Treatment is taken as a daily oral tablet. Brain imaging is typically performed to assess for brain metastases before or at the start of treatment. Your oncologist will discuss the expected side effects, monitoring schedule, and what to watch for.
If the result is negative, ALK inhibitor therapy is not indicated. The full molecular profile will be reviewed, and treatment will be planned based on other findings, including PD-L1 expression, other targetable mutations, and disease stage.
If the result is equivocal, Additional testing will be performed before treatment decisions are made. This should not significantly delay the start of treatment in most cases.
During treatment: Response to ALK inhibitor therapy is typically assessed with CT scanning at regular intervals. If the cancer progresses, repeat molecular testing will be recommended to identify the resistance mechanism and guide the next step.

Questions to ask your doctor

Has my tumour been tested for ALK rearrangements? If so, what method was used, and what was the result?
If my ALK test is positive, which ALK inhibitor is recommended for me, and why?
Does my tumour have brain metastases, and how does that affect the choice of ALK inhibitor?
What side effects should I expect from ALK inhibitor therapy, and how are they managed?
How often will scans be done to monitor my response to treatment?
If my cancer progresses on an ALK inhibitor, will re-testing be done to find out why?
Are there other driver mutations in my tumour besides ALK?
Are there clinical trials studying new ALK-targeted treatments that I might qualify for?