{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T03:35:06Z","timestamp":1789011306806,"version":"build-2803163510"},"reference-count":32,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T00:00:00Z","timestamp":1662940800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The detection of ROS1 and ALK rearrangements is performed for advanced-stage non-small cell lung cancer. Several techniques can be used on cytological samples, such as immunocytochemistry (ICC), fluorescence in situ hybridization (FISH) and, more recently, next-generation sequencing (NGS), which is gradually becoming the gold standard. We performed a retrospective study to compare ALK and ROS1 rearrangement results from immunocytochemistry, FISH and NGS methods from 131 cytological samples. Compared to NGS, the sensitivity and specificity of ICC were 0.79 and 0.91, respectively, for ALK, and 1 and 0.87 for ROS1. Regarding FISH, the sensitivity and specificity were both at 1 for ALK and ROS1 probes. False-positive cases obtained by ICC were systematically corrected by FISH. When using ICC and FISH techniques, results are very close to NGS. The false-positive cases obtained by ICC are corrected by FISH, and the true-positive cases are confirmed. NGS has the potential to improve the detection of ALK and ROS1 rearrangements in cytological samples; however, the cost of this technique is still much higher than the sequential use of ICC and FISH.<\/jats:p>","DOI":"10.3390\/ijms231810556","type":"journal-article","created":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T22:53:46Z","timestamp":1663023226000},"page":"10556","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Comparison between Immunocytochemistry, FISH and NGS for ALK and ROS1 Rearrangement Detection in Cytological Samples"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3321-6951","authenticated-orcid":false,"given":"Diane","family":"Frankel","sequence":"first","affiliation":[{"name":"Aix Marseille Univ, APHM, INSERM, MMG, H\u00f4pital la Timone, Service de Biologie Cellulaire, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Nanni","sequence":"additional","affiliation":[{"name":"APHM, Facult\u00e9 de M\u00e9decine Nord, Service d\u2019Oncobiologie, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L\u2019Houcine","family":"Ouafik","sequence":"additional","affiliation":[{"name":"APHM, Facult\u00e9 de M\u00e9decine Nord, Service d\u2019Oncobiologie, 13015 Marseille, France"},{"name":"Aix Marseille Univ, CNRS, INP, Inst Neurophysiopathol, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara","family":"Camilla","sequence":"additional","affiliation":[{"name":"APHM, Facult\u00e9 de M\u00e9decine Nord, Service d\u2019Oncobiologie, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2422-5947","authenticated-orcid":false,"given":"Eric","family":"Pellegrino","sequence":"additional","affiliation":[{"name":"APHM, Facult\u00e9 de M\u00e9decine Nord, Service d\u2019Oncobiologie, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Beaufils","sequence":"additional","affiliation":[{"name":"APHM, Facult\u00e9 de M\u00e9decine Nord, Service d\u2019Oncobiologie, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5807-9503","authenticated-orcid":false,"given":"Laurent","family":"Greillier","sequence":"additional","affiliation":[{"name":"Multidisciplinary Oncology and Therapeutic Innovations, Marseille University Hospital (APHM), Aix Marseille University, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herv\u00e9","family":"Dutau","sequence":"additional","affiliation":[{"name":"Department of Thoracic Oncology, Pleural Diseases and Interventional Pulmonology, APHM, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3988-1792","authenticated-orcid":false,"given":"Philippe","family":"Astoul","sequence":"additional","affiliation":[{"name":"Department of Thoracic Oncology, Pleural Diseases and Interventional Pulmonology, APHM, 13015 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0458-5109","authenticated-orcid":false,"given":"Elise","family":"Kaspi","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, APHM, INSERM, MMG, H\u00f4pital la Timone, Service de Biologie Cellulaire, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0045-5641","authenticated-orcid":false,"given":"Patrice","family":"Roll","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, APHM, INSERM, MMG, H\u00f4pital la Timone, Service de Biologie Cellulaire, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,12]]},"reference":[{"key":"ref_1","unstructured":"(2022, April 29). Cancer Today. Available online: http:\/\/gco.iarc.fr\/today\/home."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"321","DOI":"10.5858\/arpa.2017-0388-CP","article-title":"Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment with Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology","volume":"142","author":"Lindeman","year":"2018","journal-title":"Arch. Pathol. Lab. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1200\/JCO.2011.35.6345","article-title":"ROS1 Rearrangements Define a Unique Molecular Class of Lung Cancers","volume":"30","author":"Bergethon","year":"2012","journal-title":"J. Clin. Oncol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1822","DOI":"10.1093\/annonc\/mdt071","article-title":"ROS1 Fusions in Chinese Patients with Non-Small-Cell Lung Cancer","volume":"24","author":"Cai","year":"2013","journal-title":"Ann. Oncol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1097\/JTO.0000000000000232","article-title":"Clinical and the Prognostic Characteristics of Lung Adenocarcinoma Patients with ROS1 Fusion in Comparison with Other Driver Mutations in East Asian Populations","volume":"9","author":"Chen","year":"2014","journal-title":"J. Thorac. Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5216","DOI":"10.1158\/1078-0432.CCR-09-0802","article-title":"Unique Clinicopathologic Features Characterize ALK-Rearranged Lung Adenocarcinoma in the Western Population","volume":"15","author":"Rodig","year":"2009","journal-title":"Clin. Cancer Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/nature05945","article-title":"Identification of the Transforming EML4-ALK Fusion Gene in Non-Small-Cell Lung Cancer","volume":"448","author":"Soda","year":"2007","journal-title":"Nature"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1002\/dc.23318","article-title":"ALK and ROS1 Rearrangements Tested by Fluorescence in Situ Hybridization in Cytological Smears from Advanced Non-Small Cell Lung Cancer Patients","volume":"43","author":"Bozzetti","year":"2015","journal-title":"Diagn. Cytopathol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1097\/JTO.0000000000000465","article-title":"Comparison of Methods in the Detection of ALK and ROS1 Rearrangements in Lung Cancer","volume":"10","author":"Rogers","year":"2015","journal-title":"J. Thorac. Oncol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1016\/j.jtho.2015.12.111","article-title":"ALK Protein Analysis by IHC Staining after Recent Regulatory Changes: A Comparison of Two Widely Used Approaches, Revision of the Literature, and a New Testing Algorithm","volume":"11","author":"Marchetti","year":"2016","journal-title":"J. Thorac. Oncol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1016\/j.annonc.2020.07.014","article-title":"Recommendations for the Use of Next-Generation Sequencing (NGS) for Patients with Metastatic Cancers: A Report from the ESMO Precision Medicine Working Group","volume":"31","author":"Mosele","year":"2020","journal-title":"Ann. Oncol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1002\/cncy.21899","article-title":"ALK and ROS1 Testing on Lung Cancer Cytologic Samples: Perspectives","volume":"125","author":"Pisapia","year":"2017","journal-title":"Cancer Cytopathol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.annpat.2018.12.003","article-title":"Mise en \u00e9vidence du r\u00e9arrangement d\u2019ALK et ROS1 en immunocytochimie sur liquides de ponction","volume":"39","author":"Frankel","year":"2019","journal-title":"Ann. Pathol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/annonc\/mdy333","article-title":"Impact of TP53 Mutation Status on Systemic Treatment Outcome in ALK-Rearranged Non-Small-Cell Lung Cancer","volume":"29","author":"Kron","year":"2018","journal-title":"Ann. Oncol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.5858\/arpa.2016-0117-RA","article-title":"Preanalytic Variables in Cytology: Lessons Learned From Next-Generation Sequencing-The MD Anderson Experience","volume":"140","author":"Stewart","year":"2016","journal-title":"Arch. Pathol. Lab. Med."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1111\/cas.12081","article-title":"Importance of the Cytological Samples for the Epidermal Growth Factor Receptor Gene Mutation Test for Non-Small Cell Lung Cancer","volume":"104","author":"Hagiwara","year":"2013","journal-title":"Cancer Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1002\/cncy.21771","article-title":"Cytology Smears as Excellent Starting Material for Next-Generation Sequencing-Based Molecular Testing of Patients with Adenocarcinoma of the Lung","volume":"125","author":"Velizheva","year":"2017","journal-title":"Cancer Cytopathol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1136\/jclinpath-2021-207490","article-title":"Molecular Diagnosis in Non-Small-Cell Lung Cancer: Expert Opinion on ALK and ROS1 Testing","volume":"75","author":"Conde","year":"2022","journal-title":"J. Clin. Pathol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3334","DOI":"10.1158\/1078-0432.CCR-17-2452","article-title":"Resistance Mechanisms to Targeted Therapies in ROS1+ and ALK+ Non-Small Cell Lung Cancer","volume":"24","author":"McCoach","year":"2018","journal-title":"Clin. Cancer Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1007\/s40291-019-00389-y","article-title":"Clinicopathological Features of ALK Expression in 9889 Cases of Non-Small-Cell Lung Cancer and Genomic Rearrangements Identified by Capture-Based Next-Generation Sequencing: A Chinese Retrospective Analysis","volume":"23","author":"Zhao","year":"2019","journal-title":"Mol. Diagn. Ther."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Sabir, S.R., Yeoh, S., Jackson, G., and Bayliss, R. (2017). EML4-ALK Variants: Biological and Molecular Properties, and the Implications for Patients. Cancers, 9.","DOI":"10.3390\/cancers9090118"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1007\/s00432-020-03166-1","article-title":"ALK Detection in Lung Cancer: Identification of Atypical and Cryptic ALK Rearrangements Using an Optimal Algorithm","volume":"146","author":"Liu","year":"2020","journal-title":"J. Cancer Res. Clin. Oncol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1136\/jclinpath-2021-207408","article-title":"IHC versus FISH versus NGS to Detect ALK Gene Rearrangement in NSCLC: All Questions Answered?","volume":"75","author":"Batra","year":"2022","journal-title":"J. Clin. Pathol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1097\/JTO.0b013e3181fb7cd6","article-title":"Increased ALK Gene Copy Number and Amplification Are Frequent in Non-Small Cell Lung Cancer","volume":"6","author":"Salido","year":"2011","journal-title":"J. Thorac. Oncol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1002\/cncy.21844","article-title":"Accuracy of Next-Generation Sequencing for the Identification of Clinically Relevant Variants in Cytology Smears in Lung Adenocarcinoma","volume":"125","author":"Baum","year":"2017","journal-title":"Cancer Cytopathol."},{"key":"ref_26","first-page":"3495","article-title":"Multiplexed Molecular Profiling of Lung Cancer with Malignant Pleural Effusion Using next Generation Sequencing in Chinese Patients","volume":"19","author":"Ruan","year":"2020","journal-title":"Oncol. Lett."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.3892\/ijo.2017.3935","article-title":"Routine Genetic Testing of Lung Cancer Specimens Derived from Surgery, Bronchoscopy and Fluid Aspiration by next Generation Sequencing","volume":"50","author":"Yamamoto","year":"2017","journal-title":"Int. J. Oncol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1515\/cclm-2017-0527","article-title":"Detection of EGFR, KRAS and BRAF Mutations in Metastatic Cells from Cerebrospinal Fluid","volume":"56","author":"Frankel","year":"2018","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Schluckebier, L., Caetano, R., Garay, O.U., Montenegro, G.T., Custodio, M., Aran, V., and Gil Ferreira, C. (2020). Cost-Effectiveness Analysis Comparing Companion Diagnostic Tests for EGFR, ALK, and ROS1 versus next-Generation Sequencing (NGS) in Advanced Adenocarcinoma Lung Cancer Patients. BMC Cancer, 20.","DOI":"10.1186\/s12885-020-07240-2"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3268","DOI":"10.3390\/curroncol28050284","article-title":"Reflex ROS1 IHC Screening with FISH Confirmation for Advanced Non-Small Cell Lung Cancer-A Cost-Efficient Strategy in a Public Healthcare System","volume":"28","author":"Makarem","year":"2021","journal-title":"Curr. Oncol."},{"key":"ref_31","first-page":"208034","article-title":"Biomarker Testing Strategies in Non-Small Cell Lung Cancer in the Real-World Setting: Analysis of Methods in the Prospective Central Lung Cancer Biomarker Registry (LungPath) from the Spanish Society of Pathology (SEAP)","volume":"13","author":"Rojo","year":"2021","journal-title":"J. Clin. Pathol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1007\/978-1-0716-1278-1_12","article-title":"Immunocytochemical Detection of ALK and ROS1 Rearrangements in Lung Cancer Cytological Samples","volume":"2279","author":"Frankel","year":"2021","journal-title":"Methods Mol. Biol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/18\/10556\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:29:42Z","timestamp":1760142582000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/18\/10556"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,12]]},"references-count":32,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["ijms231810556"],"URL":"https:\/\/doi.org\/10.3390\/ijms231810556","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,12]]}}}