Detection Of ALK Rearrangements Research Articles

Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer.

Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.

Comparison of two immunohistochemical staining protocols for ALK demonstrates non-inferiority of a 5A4 clone-based protocol versus an ALK01 clone-based protocol for the diagnosis of ALK + anaplastic large cell lymphoma

Detection of ALK rearrangement and/or expression of the ALK protein is an essential component in the evaluation of many neoplasms. Variability has been reported in the ability of different antibody clones to detect ALK expression. The ALK01 clone is commonly used to detect ALK expression in ALK-positive anaplastic large cell lymphoma (ALK + ALCL). However, this clone has been shown to lack sensitivity when used for solid tumors. The aim of this study was to determine if our high-sensitivity 5A4-based immunohistochemistry protocol is non-inferior to our ALK01-based protocol for the detection of ALK expression in ALK + ALCL. To compare the two protocols, we stained tissue microarrays of 126 hematolymphoid neoplasms and an additional 21 primary cutaneous ALK-negative anaplastic large cell lymphomas with both protocols. All 28 ALK + ALCL samples that were positive for the ALK01 antibody were also positive for the 5A4 clone. Three cases on the tissue microarray that were negative with the ALK01 antibody were clearly positive with the 5A4 antibody. We subsequently stained whole tissue sections of these three cases with the ALK01 antibody and found that these three cases were indeed positive with the ALK01 protocol, suggesting that the absence of staining on the tissue microarray samples was due to a combination of sampling error as well as a dimmer signal with the ALK01 protocol. Our study demonstrates that our 5A4-based protocol is non-inferior to the ALK01 antibody for the diagnosis of ALK-positive anaplastic large cell lymphoma, thus allowing our laboratory to discontinue the use of the ALK01-based protocol.

Targeting ALK in Neuroendocrine Tumors of the Lung.

BackgroundAnaplastic lymphoma kinase (ALK) rearrangements are known oncogenic drivers in non-small cell lung cancer (NSCLC). Few case reports described the occurrence of such rearrangements in large cell neuroendocrine carcinomas (LCNECs) of the lung without information on clinical responses to ALK tyrosine kinase inhibitors (TKIs) in these cases. Currently, neuroendocrine tumors of the lungs are not screened for ALK rearrangements.MethodsTo illustrate the clinical impact of molecular characterization in LCNECs, we report the disease course in three patients with ALK-rearranged metastatic LCNEC from our clinical routine, as well as their treatment response to ALK TKIs (index cases). To gain insight into the prevalence of ALK rearrangements in neuroendocrine tumors of the lung, we analyzed a retrospective cohort of 436 tumor biopsies including LCNEC (n = 61), small cell lung cancer (SCLC) (n = 206), typical (n = 91) and atypical (n = 69) carcinoids, and mixed histology (n = 9) for the presence of ALK rearrangements using a sequential diagnostic algorithm. ALK immunohistochemistry (IHC) was evaluable in 362 cases; fluorescence in situ hybridization (FISH) was evaluable in 28 out of the 35 IHC-positive cases, followed by next-generation sequencing (NGS) that was available in 12 cases.ResultsWithin the retrospective cohort, ALK IHC was positive in 35 out of 362 (9.7%) evaluable samples. FISH was positive in 3 out of the 28 (10.7%) evaluable cases: 2 with atypical carcinoids and 1 with LCNEC. Additionally, the 3 index cases showed positive ALK IHC, which was confirmed by NGS. Within the retrospective cohort, NGS confirmed the presence of an ALK genomic rearrangement in one FISH-positive atypical carcinoid where material was sufficient for sequencing. Two out of three patients with metastatic ALK-rearranged LCNEC received up-front treatment with the ALK TKI alectinib and showed rapid tumor response at all metastatic sites, including multiple brain metastases.ConclusionsALK rearrangements represent rare but targetable oncogenic driver alterations in LCNEC. Contrarily to NSCLC, the detection of ALK rearrangements in neuroendocrine tumors of the lung is challenging, since ALK IHC can lead to false-positive results and therefore needs confirmation by FISH or NGS. Up-front comprehensive molecular profiling with NGS should be performed in metastatic LCNEC in order not to miss actionable genomic alterations.

P59.27 Complementary Utility of Combined ALK/ROS1 FISH with Immunohistochemistry for ALK/ROS1 Rearrangement Testing in Lung Cancer

Testing for EGFR mutations, ALK and ROS1 rearrangements and BRAF mutations are now recommended as the essential minimum predictive biomarkers to be tested in primary non-squamous NSCLC patients presenting with advanced disease. While the ALK D5F3 Ventana immunohistochemistry (IHC) Assay is approved for detection of ALK rearrangements and for targeted therapy, ROS1 IHC only serves as a screening tool for ROS1 rearrangements with demonstration of gene fusions by molecular methods required for confirmation and targeted treatment. Nevertheless, equivocal IHC results, although uncommon, still occur with the D5F3 ALK assay necessitating complementary methods for confirmation. The recent availability of combined ALK/ROS1 break-apart fluorescence in-situ hybridisation (FISH) probes offer the advantage of tissue conservation with ability to analyse both gene alterations in a single tissue section. The aim of the present study was to study the utility of the combined ALK/ROS1 FISH assay as a complement to ALK and ROS1 IHC in routine predictive biomarker testing algorithms. Over a 6-year study period, all EGFR wild type NSCLC samples were subject to automated ALK D5F3 Ventana IHC assay and ROS1 IHC using the D4D6 (Cell signalling technology) clone as a manual lab developed test. Diffuse strong granular staining in tumor cells for ALK and ROS1 protein was interpreted as positive. All cases of equivocal ALK staining and positive ROS1 staining was subject to combined ALK/ROS1 FISH using the FlexISH ALK/ROS1 DistinguISH Probe (Vysis) performed as per manufacturers’ instructions. Presence of ALK/ROS1 break apart signals and/or isolated ALK/ROS1 3’ signals in >15% of interpretable tumour nuclei was considered as positive for ALK or ROS1 rearrangement. The ALK Ventana Assay was performed in 711 formalin fixed paraffin embedded EGFR wild type NSCLC samples including biopsies, lymph node excisions and cell blocks. Of these, 12% (85/711) were positive, 2% (13/711) were equivocal, 75% (539/711) were negative, while in the remaining 11% (76/711), result could not be evaluated due to exhaustion of tumor tissue. FISH analysis in four of the ALK IHC equivocal cases show absence of ALK translocations while no tissue remained for FISH analysis in the remaining equivocal cases. ROS1 IHC was performed in 434 cases of the above cohort of which 7% (30/434) were positive. ROS1 immunopositivity was enriched among ALK IHC positive cases with 43% (19/44) of ALK IHC positive cases also showing protein expression of ROS1. FISH analysis revealed ROS1 translocation in two cases (both showing diffuse strong ROS1 protein expression and negative ALK IHC) while all dual ALK/ROS IHC positive cases tested by FISH showed presence of only ALK rearrangements with non-rearranged ROS1 signals. Tissue adequacy remains the major limiting factor for predictive biomarker testing in lung cancer. The use of combined ALK-ROS FISH allows for excellent demonstration of ALK and ROS1 rearrangements in the same section using the same criteria validated in single gene break apart FISH probes. ROS1 protein is commonly overexpressed in ALK rearranged NSCLC and may represent cross reactivity with ALK or a related protein.

Abstract 468: Feasibility of digital PCR for the detection of ALK rearrangement in the plasma of non-small cell lung cancer patients

Abstract Introduction: Currently, the three primary methods of detecting ALK rearrangement are fluorescent in situ hybridization, immunohistochemistry, and reverse transcriptase-polymerase chain reaction (RT-PCR). The former two methods use tissue as the laboratory materials, but some patients do not have sufficient tissue to perform the tests. The RT-PCR method can be conducted by both tissue and blood, but its detection of ALK rearrangement seems not sensitive enough. Digital PCR (dPCR) is a biotechnology refinement of conventional PCR methods that may be a more precise method than RT-PCR. Materials and Methods: An EML4-ALK variant 1 (v1) synthetic sequence, a variant 2 (v2) synthetic sequence, and a variant 3 (v3) non-small cell lung cancer (NSCLC) cell line (NCI-H2228) were used to evaluate the performance of our dPCR assay. To examine the performance PCR on clinical samples, we used both dPCR and RT-PCR assays to quantify the expression levels of EML4-ALK variants (v1, v2, and v3) in the circulating tumor RNAs derived from 414 plasma samples of 30 NSCLC patients during their ALK inhibitor treatment. Results: We have designed a multiplex dPCR assay for the detection of EML4-ALK in a v1 synthetic sequence (with 8,000 copies), a v2 synthetic sequence (with 10,000 copies), and a v3 cell line (with 100 copies). Our results showed high specificities and precisions (8,757 ± 592 copies, 11,070 ± 7,791 copies, and 93 ± 14 copies, respectively) for detecting all three variants simultaneously. On the other hand, our results observed good linearities (R2 = 0.9996, 0.9985, and 0.9991, respectively) in all three variants. To determine our dPCR assay's limit of detection for v1 and v2 synthetic sequences (each with four copies), our assay successfully measured the copy numbers of both v1 and v2 (4.1 ± 1.6 and 3.9 ± 1.8 copies, respectively). Comparing the sensitivities of our dPCR assay with RT-PCR assay, dPCR was able to detect down to 2 copies (for v1 and v2) and 20 pg of cDNA (for v3) while RT-PCR could only detect 200 copies (for v1 and v2) and 200 pg of cDNA (for v3). After confirming the promising performance of our dPCR assay, we tried to detect EML4-ALK variants by both dPCR and RT-PCR assays in the plasma samples of our recruited patients but mostly negative. Only one sample detected 39.2 copies of EML4-ALK v3 using dPCR assay. Conclusion: dPCR assay is a precise method with good performance at detecting EML4-ALK variants in synthetic sequences and cell line, which is more sensitive than RT-PCR. However, EML4-ALK variants could not be detected in the majority of our plasma samples. This may be due to insufficient circulating RNAs for detection. In addition, RNA may be degraded by RNase in plasma and that platelet may be a better alternative than plasma for the detection of RNAs in patient samples. Additional testing is warranted to detect EML4-ALK variants in the platelet samples of another NSCLC patient cohort. Citation Format: William C. Cho, Alvin H. Fong, King Y. Fung, Jeannie Y. Chik, Jacky Y. Li. Feasibility of digital PCR for the detection of ALK rearrangement in the plasma of non-small cell lung cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 468.

P37.21 Improvement of PCR-Based Detection of ALK Rearrangements

ALK fusions can be detected by FISH (florescence is situ hybridization), IHC (immunohistochemistry), RT-PCR (reverse transcription polymerase chain reaction) and NGS (next generation sequencing). All these methods have advantages and drawbacks. We aimed to improve the performance of PCR testing, which is cost-efficient and requires minimal amount of material.

Prospective Multicenter Validation of the Detection of ALK Rearrangements of Circulating Tumor Cells for Noninvasive Longitudinal Management of Patients With Advanced NSCLC

IntroductionPatients with advanced-stage NSCLC whose tumors harbor an ALK gene rearrangement benefit from treatment with multiple ALK inhibitors (ALKi). Approximately 30% of tumor biopsy samples contain insufficient tissue for successful ALK molecular characterization. This study evaluated the added value of analyzing circulating tumor cells (CTCs) as a surrogate to ALK tissue analysis and as a function of the response to ALKi. MethodsWe conducted a multicenter, prospective observational study (NCT02372448) of 203 patients with stage IIIB/IV NSCLC across nine French centers, of whom 81 were ALK positive (immunohistochemistry or fluorescence in situ hybridization [FISH]) and 122 ALK negative on paraffin-embedded tissue specimens. Blood samples were collected at baseline and at 6 and 12 weeks after ALKi initiation or at disease progression. ALK gene rearrangement was evaluated with CTCs using immunocytochemistry and FISH analysis after enrichment using a filtration method. ResultsAt baseline, there was a high concordance between the detection of an ALK rearrangement in the tumor tissue and in CTCs as determined by immunocytochemistry (sensitivity, 94.4%; specificity 89.4%). The performance was lower for the FISH analysis (sensitivity, 35.6%; specificity, 56.9%). No significant association between the baseline levels or the dynamic change of CTCs and overall survival (hazard ratio = 0.59, 95% confidence interval: 0.24–1.5, p = 0.244) or progression-free survival (hazard ratio = 0.84, 95% confidence interval: 0.44–1.6, p = 0.591) was observed in the patients with ALK-positive NSCLC. ConclusionsCTCs can be used as a complementary tool to a tissue biopsy for the detection of ALK rearrangements. Longitudinal analyses of CTCs revealed promise for real-time patient monitoring and improved delivery of molecularly guided therapy in this population.

Abstract 5299: Detection of ALK fusion transcripts in plasma of non-small cell lung cancer patients using a novel RT-PCR based assay

Abstract Background and objective: Detection of genomic rearrangements like ALK fusions are of great interest in non-small cell lung cancer (NSCLC) as those alterations can be targeted by an increasing number of drugs. To overcome tissue limitations, detection of these alterations from liquid biopsies is an unmet need, despite the development of novel NGS-based tests. To allow the detection of ALK rearrangements from circulating-free RNA (cfRNA) from NSCLC patients, we have evaluated a novel RT-PCR based assay and compared the results to tissue-based testing using immunohistochemistry (IHC) or fluorescence in-situ hybridization (FISH). Materials and Methods: Sixty-five patients with late stage NSCLC were included in the study. ALK status was assessed on tissue section using immunohistochemistry and/or FISH. cfRNA was extracted from 2 ml of plasma from EDTA or Streck BCT DNA tubes using a prototype cfRNA Sample Preparation method (Roche Molecular Systems, Pleasanton, CA). For the detection of ALK-rearrangements from plasma, a prototype ALK/RET/ROS1 Fusion Panel assay (Roche) was used. Results: The analytical sensitivity of the assay was evaluated by testing plasma from healthy individuals spiked with RNA extracted from FFPE tissue section of an ALK positive tumor. Positive results were obtained with samples spiked with as little as 3 ng RNA. Of the forty-five ALK-fusion positive patients, 11 patients were already under anti-ALK therapy and in none of the patients an ALK fusion could be detected. However, of five samples tested at progression, two (40%) were tested positive. For the 29 ALK-fusion positive samples which were included at baseline prior to therapy, 11 samples have been tested positive for ALK fusions (38%). All 20 negative controls were negative using the PCR based assay. Consequently, the key test parameters for samples tested at baseline were: sensitivity = 37.93% [95% CI 20.69% - 57.74%]; specificity = 100.00% [95% 83.16% - 100.00%]; positive predictive value = 100%; negative predictive value weighted for a prevalence of ALK fusions of 4% in metastatic NSCLC patients = 97.48% [95% CI 96.68 - 98.09]. Conclusion: The prototype cobas ALK/RET/ROS1 Fusion Panel assay was able to detect ALK fusion transcripts in the plasma of NSCLC patients at baseline as well as at disease progression. Limited sensitivity could be explained by biological factors influencing nucleic acid shedding by tumours, as well as the presence of fusions not covered by the assay. However, the assay demonstrated high specificity. These data demonstrate that this assay could potentially be used to select patients for an anti-ALK therapy when tissue samples are not available. Citation Format: Simon Heeke, Marius Ilié, Maryline Allegra, Audrey Vallée, Carole Salacroup, Virginie Tanga, Véronique Hofman, Jaya Rajamani, Michael Lee, Ellen Ordinario, Marc G. Denis, Paul Hofman. Detection of ALK fusion transcripts in plasma of non-small cell lung cancer patients using a novel RT-PCR based assay [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5299.

Continual Improvement of the Reliability of EML4-ALK Rearrangement Detection in Non–Small-Cell Lung Cancer: A Long-Term Comparison of ALK Detection in China

The results of EML4-ALK testing are critical to manage ALK tyrosine kinase receptor inhibitor treatment. Thus, the accurate detection of ALK rearrangement is increasingly becoming a matter of serious concern. To address this issue, a long-term EML4-ALK proficiency testing (PT) scheme was launched in China in 2015, serving as an educational tool for assessing and improving the testing quality of EML4-ALK fusion detection. Responses across 20 different PT samples interrogating three different variants and wild-type samples were collected between 2015 and 2019. Performance was analyzed by evaluating the detection methods, kits, and pre-analytic practices used to further display the landscape of changing conditions of the reliability of EML4-ALK testing. During the 5 years, 3224 results reported from 988 laboratories were evaluated, with an overall error rate of 5.36%. Along with an increasing number of participating laboratories, the error rate within each of the different methods showed a significantly downward trend over the years. No obvious differences in the error rates were found regarding the testing methods or kit manufacturers. Moreover, the individual performance of the laboratories improved when they participated in more PT scheme rounds. The data demonstrated that the performance of individual Chinese laboratories for EML4-ALK testing continuously improved over time by participating PT schemes, regardless of their method. However, care must be taken in standardized operations and validations.

P1.02 ALK Gene Rearrangement in Patients with Lung Cancer in Northern Mexican Population

EGFR mutation and re-arrangement of the ALK gene are two of the molecular targets evaluated in all cases of patients with primary lung adenocarcinoma. ALK rearrangements are mutually exclusive with mutations in EGFR or KRAS. These mutations are helpful in choosing targeted therapy for the patient. The aim of this study is to evaluate the frequency of ALK gene rearrangement in patients with Lung cancer in Northern MX population and histological patterns. 450 patients with NSLC were evaluated from 2006 to 2017. In all cases we perform immunohistochemistry with clone D3F5 in an automated platform. FISH rearrangement for ALK break apart were done a commercial kit. We follow the recommended criteria of IASLC for the evaluation of the FISH probes. Immunohistochemistry and FISH test were reviewed by 2 pathologists with experience and training in the evaluation of both test. This study includes 450 patients. The median age of the patients with ALK gene rearrangement was 53 years (range 37-82) and male to female ratio of 1:8. 65 (14.44%) were positive by inmmunohistochemistry in any intensity and percentage of neoplastic cells, and only 17 (3.77%) were positive or ALK rearrangement by FISH. All the cases which was negative for immunohistochemistry was negative by FISH. We found ALK rearrangements in 17 cases (3.77%), this figure is similar in Hispanic resident in US and Latin-American population, however reports in Mexican population are between 4 and 10.5 %. This difference it will be due to different cohorts of patients, methodology types of FISH probes used for the detection of ALK rearrangements and ethnic differences.

Gene fusion involving the insulin‐like growth factor 1 receptor in an ALK‐negative inflammatory myofibroblastic tumour

Inflammatory myofibroblastic tumour (IMT) is a soft tissue tumour primarily affecting children and young adults. Approximately 50% of IMTs have gene fusions involving the receptor tyrosine kinase (RTK)-encoding ALK gene, providing a molecular rationale for treating IMT patients with unresectable tumours with tyrosine kinase inhibitors (TKI). However, a subset of IMT instead displays fusions affecting other RTKencoding genes, so far including NTRK3, PDGFRB and ROS1. Also, IMTs with variant RTK fusions may respond well to TKI treatment, but can be dif?cult to identify as they are negative for ALK staining at immunohistochemistry, the standard method for detection of ALK rearrangements. We used RNA-sequencing to search for alternate fusion events in an ALK-negative IMT. We found a novel fusion gene - FN1-IGF1R. The FN1 gene, encoding ?bronectin, is thought to provide a strong promoter activity for the kinase domain of the RTK insulin-like growth factor 1 receptor, a mechanism similar to previously described RTK fusions in IMT.

Three-dimensional nanostructured substrates enable dynamic detection of ALK-rearrangement in circulating tumor cells from treatment-naive patients with stage III/IV lung adenocarcinoma

BackgroundCirculating tumor cells (CTC) shows great prospect to realize precision medicine in cancer patients.MethodsWe developed the NanoVelcro Chip integrating three functional mechanisms. NanoVelcro CTC capture efficiency was tested in stage III or IV lung adenocarcinoma. Further, ALK-rearrangement status was examined through fluorescent in situ hybridization in CTCs enriched by NanoVelcro.ResultsNanoVelcro system showed higher CTC-capture efficiency than CellSearch in stage III or IV lung adenocarcinoma. CTC counts obtained by both methods were positively correlated (r = 0.45, p < 0.05). Further, Correlation between CTC counts and pTNM stage determined by NanoVelcro was more significant than that determined by CellSearch (p < 0.001 VS p = 0.029). All ALK-positive patients had 3 or more ALK-rearranged CTC per ml of blood. Less than 3 ALK-rearranged CTC was detected in ALK-negative patients. NanoVelcro can detect the ALK–rearranged status with consistent sensitivity and specificity compared to biopsy test. Furthermore, the ALK-rearranged CTC ratio correlated to the pTNM stage in ALK-positive patients. Following up showed that CTCs counting by NanoVelcro was more stable and reliable in evaluating the efficacy of Clozotinib both in the short and long run compared with CellSearch. Changing of NanoVlecro CTC counts could accurately reflect disease progression.ConclusionNanoVelcro provides a sensitive method for CTC counts and characterization in advanced NSCLC. ALK-rearrangement can be detected in CTCs collected from advanced NSCLC patients by NanoVelcro, facilitating diagnostic test and prognosis analysis, most importantly offering one noninvasive method for real-time monitoring of treatment reaction.

P15 Prevalence of EML4- ALK Fusion Gene in Adenocarcinoma Lung Patients by Using Immuno Histo Chemistry

An oral ATP- competitive TKI of ALK and c- MET, Crizotinib has shown impressive clinical activity in advanced non–small cell lung cancers especially in the tumors harboring ALK rearrangements. With FISH as the mainstay for detection of ALK rearrangements, the ALK Break Apart FISH Probe Kit (Abbott Molecular, Des Plaines, IL) has become an FDA-approved companion diagnostic for targeted therapy with the ALK inhibitor crizotinib in lung cancers. The objective of this molecular epidemiological study is to estimate the prevalence of EML4-ALK fusion gene using IHC as a cost effective alternative to FISH for Indian patients with adenocarcinoma lung. Patients with NSCLC, adenocarcinoma histology, whose tumors had been tested for EML4-ALK fusion gene using IHC were considered for this study. Permission was obtained from the Ethics committee before the start of the study. Clinical characteristics and treatment details were collected from the patient’s medical records. IHC analysis was performed using a Ventana automated immunostainer (Ventana Medical Systems, Illkirch Graffenstaden, France). Detection was performed using a multimer-technology system with the UltraView Universal DAB detection kit. A total of 204 NSCLC adenocarcinoma patients were included in the study. There were 126 (61.7%) men and 78 (38.23%) women with a median age of 57 years. Of the 204 patients, 47 (23.03%) were non-smokers and 175 (85.78%) had stage-IV disease at the time of initial diagnosis. 48 (23.52%) blocks were positive for EGFR mutations whereas 156 (76.47%) were EGFR wild type. EML4-ALK fusion gene was present in 27 (13.23%) patients whereas 177 (86.76%) tumors were EML4-ALK negative. 25 out of the 27 patients with ALK positivity received Crizotinib therapy. The incidence of EML4-ALK gene fusions (13.23%) in this Indian population is four fold high than the previous reported incidences and supports the claim of several recent studies that a relatively new ALK clone, 5A4 and D5F3 from cell signaling technology (Ventana) can accurately identify ALK rearranged lung ACA as compared to FISH. The inclusion of IHC for the detection of EML4-ALK gene fusions as a low cost alternative seems warranted.

164P Feasibility of liquid biopsy using plasma and platelets for detection of ALK rearrangements in non-small cell lung cancer

164P Feasibility of liquid biopsy using plasma and platelets for detection of ALK rearrangements in non-small cell lung cancer

Targeted next-generation-sequencing for reliable detection of targetable rearrangements in lung adenocarcinoma—a single center retrospective study

Oncogenic rearrangements leading to targetable gene fusions are well-established cancer driver events in lung adenocarcinoma. Accurate and reliable detection of these gene fusions is crucial to select the appropriate targeted therapy for each patient. We compared the targeted next-generation-sequencing Oncomine Focus Assay (OFA; Thermo Fisher Scientific) with conventional ALK FISH and anti-Alk immunohistochemistry in a cohort of 52 lung adenocarcinomas (10 ALK rearranged, 18 non-ALK rearranged, and 24 untested cases). We found a sensitivity and specificity of 100% for detection of ALK rearrangements using the OFA panel. In addition, targeted next generation sequencing allowed us to analyze a set of 23 driver genes in a single assay. Besides EML4-ALK (11/52 cases), we detected EZR-ROS1 (1/52 cases), KIF5B-RET (1/52 cases) and MET-MET (4/52 cases) fusions. All EML4-ALK, EZR-ROS1 and KIF5B-RET fusions were confirmed by multiplexed targeted next generation sequencing assay (Oncomine Solid Tumor Fusion Transcript Kit, Thermo Fisher Scientific). All cases with EML4-ALK rearrangement were confirmed by Alk immunohistochemistry and all but one by ALK FISH. In our experience, targeted next-generation sequencing is a reliable and timesaving tool for multiplexed detection of targetable rearrangements. Therefore, targeted next-generation sequencing represents an efficient alternative to time-consuming single target assays currently used in molecular pathology.

P1.01-014 Feasibility of Liquid Biopsy Using Plasma and Platelets for Detection of ALK Rearrangements in Non-Small Cell Lung Cancer

Fluorescence in situ hybridization (FISH) using tissue biopsy specimen is the gold standard for detection and confirmation of ALK rearrangement in non-small cell lung cancers (NSCLC), but it is time-consuming and labor-dependent procedure. Liquid biopsy using reverse-transcriptase polymerase chain reaction (RT-PCR) is expected to overcome these limitations, and provide an easy accessibility and frequent assessment of biomarkers. The aim of this study is to investigate the feasibility of liquid biopsy using plasma and platelets for detection of ALK rearrangement.

MA 15.04 Detection of ALK Rearrangements in Non-Small-Cell Lung Cancer (NSCLC) Patients by Liquid Biopsy

The ALK rearrangement (ALK+) is an important actionable genetic aberration of NSCLC, which is associated with high sensitivity to targeted agents such as crizotinib and alectinib. Currently, ALK+ is mainly detected by fluorescent in situ hybridization (FISH) or immunohistochemistry that strictly require the availability of tumor sample, however, in NSCLC, tumor tissue are not always valid or sufficient for testing and non-invasive analyzing methods are urgently needed. Recent years, next generation sequencing (NGS) based liquid biopsy has emerged as a useful complementary technique for the analysis of cancer genetic profile, in the present study, we aimed to evaluate the performance of liquid biopsy for the detection of ALK rearrangements in NSCLC.

Dichotomous ALK-IHC Is a Better Predictor for ALK Inhibition Outcome than Traditional ALK-FISH in Advanced Non-Small Cell Lung Cancer.

Purpose: ALK rearrangement detection using FISH is the standard test to identify patients with non-small cell lung carcinoma (NSCLC) eligible for treatment with ALK inhibitors. Recently, ALK protein expression in resectable NSCLC showed predictive value. We evaluated tumor response rate and survival after crizotinib treatment of patients with advanced NSCLC with ALK activation using both dichotomous immunohistochemical (IHC) staining and FISH.Experimental Design: Patients with stage IV NSCLC treated with crizotinib were selected. Tumor response was assessed. ALK rearrangements were detected by FISH (Vysis ALK-break-apart FISH-Probe KIT) and IHC [Ventana ALK (D5F3) CDx assay]. Cohorts of patients with ALK-FISH-positive advanced NSCLC from four other hospitals were used for validation.Results: Twenty-nine consecutive patients with ALK-positive advanced NSCLC diagnosed by FISH and/or IHC on small biopsies or fine-needle aspirations (FNA) were treated with ALK inhibitors. All ALK-IHC-positive patients responded to crizotinib except three with primary resistance. No tumor response was observed in 13 ALK-FISH-positive but ALK-IHC-negative patients. This was confirmed in an external cohort of 16 patients. Receiver operator characteristic (ROC) curves for ALK-IHC and ALK-FISH compared with treatment outcome showed that dichotomous ALK-IHC outperforms ALK-FISH [tumor response area under the curve: (AUC), 0.86 vs. 0.64, P = 0.03; progression-free survival (PFS): AUC 0.86 vs. 0.36, P = 0.005; overall survival (OS): AUC, 0.78 vs. 0.41, P = 0.01, respectively].Conclusions: Dichotomous ALK-IHC is superior to ALK-FISH on small biopsies and FNA to predict tumor response and survival to crizotinib for patients with advanced NSCLC. Our data strongly suggest adapting the guidelines and using dichotomous ALK-IHC as standard companion diagnostic test to select patients with NSCLC who benefit from ALK-targeting therapy. Clin Cancer Res; 23(15); 4251-8. ©2017 AACR.

Detection of ALK fusion transcripts in FFPE lung cancer samples by NanoString technology

BackgroundALK-rearranged lung cancers exhibit specific pathologic and clinical features and are responsive to anti-ALK therapies. Therefore, the detection of ALK-rearrangement is fundamental for personalized lung cancer therapy. Recently, new molecular techniques, such as NanoString nCounter, have been developed to detect ALK fusions with more accuracy and sensitivity.MethodsIn the present study, we intended to validate a NanoString nCounter ALK-fusion panel in routine biopsies of FFPE lung cancer patients. A total of 43 samples were analyzed, 13 ALK-positive and 30 ALK-negative, as previously detected by FISH and/or immunohistochemistry.ResultsThe NanoString panel detected the presence of the EML4-ALK, KIF5B-ALK and TFG-ALK fusion variants. We observed that all the 13 ALK-positive cases exhibited genetic aberrations by the NanoString methodology. Namely, six cases (46.15%) presented EML-ALK variant 1, two (15.38%) presented EML-ALK variant 2, two (15.38%) presented EML-ALK variant 3a, and three (23.07%) exhibited no variant but presented unbalanced expression between 5’/3’ exons, similar to other positive samples. Importantly, for all these analyses, the initial input of RNA was 100 ng, and some cases displayed poor RNA quality measurements.ConclusionsIn this study, we reported the great utility of NanoString technology in the assessment of ALK fusions in routine lung biopsies of FFPE specimens.

P1.02-053 Comparison of Two Different Commercially Available Probes for the Detection of ALK Rearrangements in Cytological Smears

Many patients with NSCLC are diagnosed at advanced stages. A high percentage of those patients have only cytological samples for morphological and molecular analysis. Furthermore ALK analysis by FISH has to be performed using a specific commercially available probe. The aim of this study is to compare two different commercially available probes for analysis of ALK gene rearrangements by FISH using cytological stained smears. We analyzed 37 cytological stained smears from 37 consecutive cases of FNA (14 Diff-Quick and 23 Papanicolau). ROSE was performed in all procedures. The status of EGFR, KRAS and BRAF was kwon in 28 patients. Two probes were used: LSI ALK BREAK APART (Vysis, Ref: 53206N38020, Izasa) was apply in all 37 cases. Additionally, in 25 of these cases we used the ZytoLight SPEC ALK Dual Color Break Apart (ZYTOVISION, Ref: Z-2124-200, Menarini Diagnostics) probe. Protocols were modified from Basel and Zytolight manufacture guidelines. In order to optimize the amount of probe and to evaluate individual nuclei, we delimited an area on each smear with no nuclear overlap. All cases were adenocarcinomas. Two cases showed ALK rearrangement (5.4%). Of the 34 negative cases, 27 were negative-polysomic (77.14%). One case was no assessable (2.7%) due to the impossibility of getting hybridization. Concordance between two probes was 100%. No differences were found between Papanicolau and DiffQuick stained smears. FISH-ALK in cytological stained smears gives excellent results. Both commercially available probes showed identical performance, both are equally valid. No differences between Papanicolau and Diff-Quick stained smears were observed. In our experience, stained cytological smears are the best choice for the analysis of ALK rearrangements in NSCLC patients, keeping paraffin for cases in which adequate cytological smears are not available.