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Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project
Gray, Steven
Introduction: The reported prevalence of ALK receptor tyrosine kinase gene (ALK) rearrangement in NSCLC ranges from 2% to 7%. The primary standard diagnostic method is fluorescence in situ hybridization (FISH). Recently, immunohistochemistry (IHC) has also proved to be a reproducible and sensitive technique. Reverse-transcriptase polymerase chain reaction (RT-PCR) has also been advocated, and most recently, the advent of targeted next-generation sequencing (NGS) for ALK and other fusions has become possible. This study compares an aplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lung scape cohort.Methods:A total of 96 cases from the European Thoracic Oncology Platform Lungscape iBiobank, with any ALK immunoreactivity were examined by FISH, central RT-PCR,and NGS. An H-score higher than 120 defines IHC positivity. RNA was extracted from the same formalin-fixed,paraffin-embedded tissues. For RT-PCR, primers coveredthe most frequent ALK translocations. For NGS, the Oncomine Solid Tumour Fusion Transcript Kit (Thermo Fisher Scientific, Waltham, MA) was used. The concordance was assessed using the Cohenk coefficient (two-sided a 5%). Results: NGS provided results for 77 of the 95 cases tested(81.1%), whereas RT-PCR provided results for 77 of 96(80.2%). Concordance occurred in 55 cases of the 60 cases tested with all four methods (43 ALK negative and 12 ALK positive). Using ALK copositivity for IHC and FISH as the criterion standard, we derived a sensitivity for RT-PCR/NGS of 70.0%/85.0%, with a specificity of 87.1%/79.0%. When either RT-PCR or NGS was combined with IHC, the sensitivity remained the same, whereas the specificity increased to 88.7% and 83.9% respectively. Conclusion: NGS evaluation with the Oncomine Solid Tumour Fusion transcript kit and RT-PCR proved to have high sensitivity and specificity, advocating their use in routine practice.For maximal sensitivity and specificity, ALK status should be assessed by using two techniques and a third one in discordant cases. We therefore propose a customizable testing algorithm.These findings significantly influence existing testing paradigms and have clear clinical and economic impact.
Keyword(s): ALK receptortyrosine kinase gene (ALK); NSCLC; NGS; RT-PCR
Publication Date:
Type: Journal article
Peer-Reviewed: Yes
Language(s): English
Institution: Trinity College Dublin
Citation(s): Letovanec, I. and Finn, S. and Zygoura, P. and Smyth, P. and Soltermann, A. and Bubendorf, L. and Speel, E.-J. and Marchetti, A. and Nonaka, D. and Monkhorst, K. and Hager, H. and Martorell, M. and Sejda, A. and Cheney, R. and Hernandez-Losa, J. and Verbeken, E. and Weder, W. and Savic, S. and Di Lorito, A. and Navarro, A. and Felip, E. and Warth, A. and Baas, P. and Meldgaard, P. and Blackhall, F. and Dingemans, A.-M. and Dienemann, H. and Dziadziuszko, R. and Vansteenkiste, J. and O'Brien, C. and Geiger, T. and Sherlock, J. and Schageman, J. and Dafni, U. and Kammler, R. and Kerr, K. and Thunnissen, E. and Stahel, R. and Peters, S. and Stahel, R.A. and Rosell, R. and Blackhall, F. and Dafni, U. and Kerr, K.M. and Molina, M.??. and Bubendorf, L. and Weder, W. and Thunnissen, E. and Peters, S. and Finn, S. and Hiltbrunner, A. and Kammler, R. and Geiger, T. and Marti, N. and Dafni, U. and Tsourti, Z. and Polydoropoulou, V. and Zygoura, P. and Finn, S. and Smyth, P. and O'Brien, C. and Gray, S. and Weder, W. and Soltermann, A. and Opitz, I. and Curioni, A. and Bubendorf, L. and Savic, S. and Lardinois, D. and Dingemans, A.-M. and Speel, E.-J.M. and Ruland, A. and Marchetti, A. and Di Lorito, A. and De Luca, G. and Malatesta, S. and Blackhall, F. and Nonaka, D. and Quinn, A.M. and Franklin, L. and Biernat, W. and Wrona, A. and Rzyman, W. and Jassem, J. and Meldgaard, P. and Hager, H. and Madsen, L.B. and Camps, C. and Martorell, M. and Jantus-Lewintre, E. and Guijarro, R. and Kerr, K.M. and Nicolson, M. and Stevenson, D.A.J. and Mathieson, W. and Baas, P. and de Jong, J. and Monkhorst, K. and Thunnissen, E. and Smit, E. and van Setten, C. and de Langen, J. and Felip, E. and Hernandez-Losa, J. and Sansano, I. and Cheney, R. and Pine, M.B. and Reid, M. and Taylor, E. and Nackaerts, K. and Dooms, C. and Wauters, E. and Van Der Borght, S. and Dienemann, H. and Muley, T. and Warth, A., Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project, Journal of Thoracic Oncology, 2018, 13, 3, 413-425
First Indexed: 2019-10-25 07:13:31 Last Updated: 2019-10-25 07:13:31