TY - JOUR
T1 - Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients
T2 - Results from the European Thoracic Oncology Platform Lungscape Project
AU - Letovanec, Igor
AU - Finn, Stephen
AU - Zygoura, Panagiota
AU - Smyth, Paul
AU - Soltermann, Alex
AU - Bubendorf, Lukas
AU - Speel, Ernst Jan M.
AU - Marchetti, Antonio
AU - Nonaka, Daisuke
AU - Monkhorst, Kim
AU - Hager, Henrik
AU - Martorell, Miguel
AU - Sejda, Aleksandra
AU - Cheney, Richard
AU - Hernandez-Losa, Javier
AU - Verbeken, Eric
AU - Weder, Walter
AU - Savic, Spasenija
AU - Di Lorito, Alessia
AU - Navarro, Atilio
AU - Felip, Enriqueta
AU - Warth, Arne
AU - Baas, Paul
AU - Meldgaard, Peter
AU - Blackhall, Fiona
AU - Dingemans, Anne Marie
AU - Dienemann, Hendrik
AU - Dziadziuszko, Rafal
AU - Vansteenkiste, Johan
AU - O'Brien, Cathal
AU - Geiger, Thomas
AU - Sherlock, Jon
AU - Schageman, Jeoffrey
AU - Dafni, Urania
AU - Kammler, Roswitha
AU - Kerr, Keith M.
AU - Thunnissen, Erik
AU - Stahel, Rolf A.
AU - Peters, Solange
AU - Rosell, Rafael
AU - Molina, Miguel Ángel
AU - Hiltbrunner, Anita
AU - Marti, Nesa
AU - Tsourti, Zoi
AU - Polydoropoulou, Varvara
AU - Gray, Steven
AU - Opitz, Isabelle
AU - Curioni, Alessandra
AU - Lardinois, Didier
AU - Mathieson, William
AU - European Thoracic Oncology Platform Lungscape Consortium
N1 - Funding Information:
This work was supported by a local grant awarded to Dr. Solange Peters at the University Hospital of Lausanne (Centre Hospitalier Universitaire Vaudois, CHUV), Lausanne, Switzerland for the reverse-transcriptase polymerase chain reaction component and RNA extraction. Reagents to perform the fusion panel testing were provided by Thermo Fisher Scientific to St. James's Hospital in Dublin, Ireland.
Publisher Copyright:
© 2017 International Association for the Study of Lung Cancer
PY - 2018/3
Y1 - 2018/3
N2 - 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 anaplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lungscape 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 covered the 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 Cohen κ coefficient (two-sided α ≤ 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.
AB - 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 anaplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lungscape 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 covered the 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 Cohen κ coefficient (two-sided α ≤ 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.
KW - ALK
KW - NGS
KW - NSCLC
KW - RT-PCR
UR - http://www.scopus.com/inward/record.url?scp=85041242224&partnerID=8YFLogxK
U2 - 10.1016/j.jtho.2017.11.117
DO - 10.1016/j.jtho.2017.11.117
M3 - Article
C2 - 29191776
AN - SCOPUS:85041242224
SN - 1556-0864
VL - 13
SP - 413
EP - 425
JO - Journal of Thoracic Oncology
JF - Journal of Thoracic Oncology
IS - 3
ER -