Identification and therapeutic evaluation of ALK rearrangements in non‐small‐cell lung cancer

Abstract

This study aimed to present a comprehensive assessment of anaplastic lymphoma kinase (ALK) rearrangements evaluated by DNA/RNA-based next-generation sequencing (NGS) and Ventana immunohistochemistry (IHC) in patients with non-small-cell lung cancer (NSCLC) and to evaluate the therapeutic outcomes of ALK tyrosine kinase inhibitor (TKI) treatment. We investigated ALK gene fusions in 14,894 patients with NSCLC using Ventana IHC and NGS, including 12,533 cases detected via DNA-based NGS and 2,361 cases using RNA-based NGS. The overall percentage agreement (OPA), positive percentage agreement (PPA), and negative percentage agreement (NPA) were calculated when comparing the results between NGS and IHC. The therapeutic responses to ALK-TKIs were also evaluated. In total, 3.50% (439/12,533) of specimens were NGS ALK-positive (NGS-p) in the DNAbased NGS cohort and 3.63% (455/12,533) were IHC ALK-positive (IHC-p). The OPA of NGS was 99.60%, whereas its PPA and NPA were 92.75 and 99.86%, respectively. In the adenocarcinoma (ADC) subcohort, the PPA was 95.69%. In the RNA-based NGS cohort, 2.20% (52/2,361) of specimens were NGS-p and 2.63% (62/2,361) were IHC-p. The OPA of NGS was 99.49%; its PPA and NPA were 82.26 and 99.96%, respectively. Thirteen patients with discordant results received ALK-TKI treatment. In the seven NGS-p/IHC-negative (IHC-n) patients, the overall response rate (ORR) was 85.4% (6/7) and the disease control rate (DCR) was 100%. In the six NGS-negative/IHC-p patients, the ORR was 66.7% (4/6) and the DCR was 100%. In summary, a high concordance of ALK gene fusion detected via NGS and IHC was observed in this study. DNA-based NGS had a higher OPA, PPA, and PPA in the ADC subcohort, whereas RNA-based NGS had a higher NPA. Overall, the results suggest that the combination of NGS and IHC can improve the accuracy of ALK fusion detection; hence, a result determination algorithm for clinical detection of ALK gene fusion was also proposed.

Replacement of ALK inhibitors as an effective strategy for reducing drug toxicity in non-small cell lung cancer patients with ALK gene rearrangement

“…The percentage distribution of specific fusion partners was similar to the results of other studies. It is noteworthy that in one case where the FAM114A1-ALK variant was detected, it was not confirmed by any of the other methods (FISH, IHC, or RT-PCR) [6]. The results showed that only the NGS method could detect all partners of the ALK gene and all their variants, and perhaps in the future, it should become the gold standard in diagnosis of ALK gene rearrangement.…”

“…FISH failed to detect EIF2AK3-ALK, PRKAR1A-ALK, and one of the EML4-ALK variants [5]. In 2022, Zhao et al [6] tested nearly 15000 patients using the NGS and IHC methods, including 12533 cases examined by DNA-based NGS and 2361 cases examined by RNA-based NGS tests. Based on DNA examination, they showed the presence of ALK gene rearrangements in 439 (3.5%) patients.…”

A narrative review of methods for the identification of ALK fusions in patients with non-small cell lung carcinoma

“…Aberrant ALK expression (i.e., rearrangement negative) has been described in lung neuroendocrine carcinomas (including small cell lung carcinomas) and neural tissue ( 22 , 55 ). Because ALK IHC is a standalone test, reviewing the H&E before scoring the ALK IHC slide is mandatory.…”

“…NGS should be performed using a clinically validated NGS panel, which ideally should include all guideline recommended biomarkers for patients with advanced NSCLC ( 6 , 7 ). Although there are no recent head-to-head comparisons of all the main available platforms using a large cohort of real-world ALK positive patients, most NGS panels should theoretically have a high performance for the detection of ALK fusions ( 21 , 22 , 29 ). From a pragmatic stand-point some comments are useful when assessing NGS options or discussing their results.…”

“…The increasing use of next generation sequencing (NGS) has identified more than 90 different fusion partners, but echinoderm microtubule-associated protein-like 4 ( EML4 ) remains the most frequent partner (approximately 85%) ( 19 , 20 ). The most commonly reported EML4-ALK fusion breakpoints are v1 (30–40%), v3a/b (30–40%) and v2 (10%) ( 10 , 20 - 22 ). The individual frequencies of non- EML4-ALK fusions are difficult to infer but there are usually below 2%: kinesin family member 5B ( KIF5B ; range, 0.4–2.2%), striatin ( STRN ; range, 1–1.4%), huntingtin interacting protein 1 ( HIP1 ; range, 1–3%) or trafficking from ER to golgi regulator ( TFG ; 1.4%) ( 21 - 28 ).…”