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

Nadezda P Velizheva,Markus P Rechsteiner,Nadejda Valtcheva,Sandra N Freiberger,Christine E Wong,Bart Vrugt,Qing Zhong,Ulrich Wagner,Holger Moch,Sven Hillinger,Isabelle Schmitt-Opitz,Alex Soltermann,Peter J Wild,Verena Tischler

doi:10.1016/j.prp.2018.02.001

Nadezda P Velizheva, Markus P Rechsteiner + Show 12 more

Open Access

https://doi.org/10.1016/j.prp.2018.02.001

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Abstract

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.

Highlights

Since its discovery in 2007, oncogenic EML4-ALK rearrangements have been intensively studied in lung cancer biology and therapy [1,2,3,4]
First line Alk kinase inhibitor therapy with crizotinib is the current standard of care in ALK rearranged lung adenocarcinoma (LUAD) with increased progression-free survival compared with conventional chemotherapy [5]
We tested a cohort of advanced lung adenocarcinomas (LUADs) (n = 52) in this retrospective validation study (Table 1)

Summary

Introduction

Since its discovery in 2007, oncogenic EML4-ALK rearrangements have been intensively studied in lung cancer biology and therapy [1,2,3,4]. Other cancer driver fusion genes in LUAD are ROS1 and RET [6,7,8]. MET splice site mutations resulting in exon 14 skipping and activation of the c-Met pathway occur in approximately 4% of LUADs [12,13]. Patients with these mutations were shown to respond to MET inhibition [14]. The aim of the present study was to investigate the performance of a RNA-based targeted NGS assay for detection of targetable fusion genes and compare the results with corresponding FISH and IHC assays

Objectives

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Conclusion