Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project.
Details
Serval ID
serval:BIB_51ABD4101BD9
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project.
Journal
Journal of thoracic oncology
Working group(s)
European Thoracic Oncology Platform Lungscape Consortium
Contributor(s)
Stahel R.A., Rosell R., Blackhall F., Dafni U., Kerr K.M., Molina M.Á., Bubendorf L., Weder W., Thunnissen E., Peters S., Finn S., Hiltbrunner A., Kammler R., Geiger T., Marti N., Dafni U., Tsourti Z., Polydoropoulou V., Zygoura P., Finn S., Smyth P., O'Brien C., Gray S., Weder W., Soltermann A., Opitz I., Curioni A., Bubendorf L., Savic S., Lardinois D., Dingemans A.M., Speel E.M., Ruland A., Marchetti A., Di Lorito A., De Luca G., Malatesta S., Blackhall F., Nonaka D., Quinn A.M., Franklin L., Biernat W., Wrona A., Rzyman W., Jassem J., Meldgaard P., Hager H., Madsen L.B., Camps C., Martorell M., Jantus-Lewintre E., Guijarro R., Kerr K.M., Nicolson M., Stevenson DAJ, Mathieson W., Baas P., de Jong J., Monkhorst K., Thunnissen E., Smit E., van Setten C., de Langen J., Felip E., Hernandez-Losa J., Sansano I., Cheney R., Pine M.B., Reid M., Taylor E., Nackaerts K., Dooms C., Wauters E., Van Der Borght S., Dienemann H., Muley T., Warth A.
ISSN
1556-1380 (Electronic)
ISSN-L
1556-0864
Publication state
Published
Issued date
03/2018
Peer-reviewed
Oui
Volume
13
Number
3
Pages
413-425
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
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.
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%).
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.
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.
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%).
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.
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.
Keywords
Anaplastic Lymphoma Kinase/genetics, Carcinoma, Non-Small-Cell Lung/pathology, Cohort Studies, Europe, Female, High-Throughput Nucleotide Sequencing/methods, Humans, Lung Neoplasms/pathology, Male, Reverse Transcriptase Polymerase Chain Reaction/methods, Thoracic Neoplasms/genetics, Thoracic Neoplasms/pathology, ALK, NGS, NSCLC, RT-PCR
Pubmed
Web of science
Create date
24/04/2018 14:52
Last modification date
20/08/2019 14:07
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